Last updated: 2025-04-10

Checks: 6 1

Knit directory: multigroup_ctwas_analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: uncommitted changes

The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20231112)

The command set.seed(20231112) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: b815d3b

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version b815d3b. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


Ignored files:
    Ignored:    .Rhistory
    Ignored:    cv/

Unstaged changes:
    Modified:   analysis/comparing_munro_susie_st.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/comparing_munro_susie_st.Rmd) and HTML (docs/comparing_munro_susie_st.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd bda6e43 XSun 2025-04-09 update
html bda6e43 XSun 2025-04-09 update
Rmd 113f5a1 XSun 2025-04-08 update
html 113f5a1 XSun 2025-04-08 update
Rmd 82784b3 XSun 2025-04-08 update
Rmd a11a4e9 XSun 2025-04-07 update
html a11a4e9 XSun 2025-04-07 update

Introduction

The Susie st models are trained here https://sq-96.github.io/multigroup_ctwas_analysis/data_weight_training_fusionscale_rsqupdated_allhaveqtl.html

The Munro’s model are from this paper https://www.nature.com/articles/s41467-024-54840-8

library(ctwas)
library(ggplot2)
library(tidyverse)

source("/project/xinhe/xsun/multi_group_ctwas/data/samplesize.R")

folder_results_munroST <- "/project/xinhe/shengqian/ctwas_GWAS_analysis/snakemake_outputs/"
folder_results_susieST <- "/project/xinhe/xsun/multi_group_ctwas/15.susie_weights/snakemake_outputs/"
folder_results_woST <- "/project/xinhe/shengqian/ctwas_GWAS_analysis/snakemake_outputs/"

# mapping_predictdb <- readRDS("/project2/xinhe/shared_data/multigroup_ctwas/weights/mapping_files/PredictDB_mapping.RDS")
# mapping_munro <- readRDS("/project2/xinhe/shared_data/multigroup_ctwas/weights/mapping_files/Munro_mapping.RDS")
# mapping_two <- rbind(mapping_predictdb,mapping_munro)

colors <- c(  "#1f77b4", "#ff7f0e", "#2ca02c", "#d62728",  "#9467bd", "#8c564b", "#e377c2", "#7f7f7f",  "#bcbd22",  "#17becf",  "#f7b6d2",  "#c5b0d5",  "#9edae5", "#ffbb78",  "#98df8a",  "#ff9896" )

plot_piechart <- function(ctwas_parameters, colors, by, title) {
  # Create the initial data frame
  data <- data.frame(
    category = names(ctwas_parameters$prop_heritability),
    percentage = ctwas_parameters$prop_heritability
  )
  
  # Split the category into context and type
  data <- data %>%
    mutate(
      context = sub("\\|.*", "", category),
      type = sub(".*\\|", "", category)
    )
  
  # Aggregate the data based on the 'by' parameter
  if (by == "type") {
    data <- data %>%
      group_by(type) %>%
      summarize(percentage = sum(percentage)) %>%
      mutate(category = type)  # Use type as the new category
  } else if (by == "context") {
    data <- data %>%
      group_by(context) %>%
      summarize(percentage = sum(percentage)) %>%
      mutate(category = context)  # Use context as the new category
  } else {
    stop("Invalid 'by' parameter. Use 'type' or 'context'.")
  }
  
  # Calculate percentage labels for the chart
  data$percentage_label <- paste0(round(data$percentage * 100, 1), "%")
  
  # Create the pie chart
  pie <- ggplot(data, aes(x = "", y = percentage, fill = category)) +
    geom_bar(stat = "identity", width = 1) +
    coord_polar("y", start = 0) +
    theme_void() +  # Remove background and axes
    geom_text(aes(label = percentage_label), 
              position = position_stack(vjust = 0.5), size = 3) +  # Adjust size as needed
    scale_fill_manual(values = colors) +  # Custom colors
    labs(fill = "Category") +  # Legend title
    ggtitle(title)  # Title
  
  return(pie)
}

LDL-ukb-d-30780_irnt

Setting: shared_all, thin = 0.1

trait <- "LDL-ukb-d-30780_irnt"
thin <- 0.1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
a11a4e9 XSun 2025-04-07

Setting: shared_all, thin = 0.5

thin <- 0.5
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
a11a4e9 XSun 2025-04-07

Setting: shared_all, thin = 1

thin <- 1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
a11a4e9 XSun 2025-04-07

Setting: shared_type, thin = 0.1

thin <- 0.1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
a11a4e9 XSun 2025-04-07

Setting: shared_type, thin = 0.5

thin <- 0.5
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
a11a4e9 XSun 2025-04-07

Setting: shared_type, thin = 1

thin <- 1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
a11a4e9 XSun 2025-04-07

IBD-ebi-a-GCST004131

Setting: shared_all, thin = 0.1

trait <- "IBD-ebi-a-GCST004131"
thin <- 0.1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
a11a4e9 XSun 2025-04-07

Setting: shared_all, thin = 0.5

thin <- 0.5
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
113f5a1 XSun 2025-04-08
a11a4e9 XSun 2025-04-07

Setting: shared_all, thin = 1

thin <- 1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
113f5a1 XSun 2025-04-08
a11a4e9 XSun 2025-04-07

Setting: shared_type, thin = 0.1

thin <- 0.1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
113f5a1 XSun 2025-04-08
a11a4e9 XSun 2025-04-07

Setting: shared_type, thin = 0.5

thin <- 0.5
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
113f5a1 XSun 2025-04-08
a11a4e9 XSun 2025-04-07

Setting: shared_type, thin = 1

thin <- 1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
113f5a1 XSun 2025-04-08
a11a4e9 XSun 2025-04-07

T2D-panukb

Setting: shared_all, thin = 0.1

trait <- "T2D-panukb"
thin <- 0.1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
a11a4e9 XSun 2025-04-07

Setting: shared_all, thin = 0.5

thin <- 0.5
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
113f5a1 XSun 2025-04-08
a11a4e9 XSun 2025-04-07

Setting: shared_all, thin = 1

thin <- 1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
113f5a1 XSun 2025-04-08
a11a4e9 XSun 2025-04-07

Setting: shared_type, thin = 0.1

thin <- 0.1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
113f5a1 XSun 2025-04-08
a11a4e9 XSun 2025-04-07

Setting: shared_type, thin = 0.5

thin <- 0.5
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
113f5a1 XSun 2025-04-08
a11a4e9 XSun 2025-04-07

Setting: shared_type, thin = 1

thin <- 1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
113f5a1 XSun 2025-04-08
a11a4e9 XSun 2025-04-07

BMI-panukb

Setting: shared_all, thin = 0.1

trait <- "BMI-panukb"
thin <- 0.1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
a11a4e9 XSun 2025-04-07

Setting: shared_all, thin = 0.5

thin <- 0.5
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
113f5a1 XSun 2025-04-08
a11a4e9 XSun 2025-04-07

Setting: shared_all, thin = 1

thin <- 1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
113f5a1 XSun 2025-04-08
a11a4e9 XSun 2025-04-07

Setting: shared_type, thin = 0.1

thin <- 0.1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
113f5a1 XSun 2025-04-08
a11a4e9 XSun 2025-04-07

Setting: shared_type, thin = 0.5

thin <- 0.5
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
113f5a1 XSun 2025-04-08
a11a4e9 XSun 2025-04-07

Setting: shared_type, thin = 1

thin <- 1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09
113f5a1 XSun 2025-04-08
a11a4e9 XSun 2025-04-07

RBC-panukb

Setting: shared_all, thin = 0.1

trait <- "RBC-panukb"
thin <- 0.1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09

Setting: shared_all, thin = 0.5

thin <- 0.5
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09

Setting: shared_all, thin = 1

thin <- 1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09

Setting: shared_type, thin = 0.1

thin <- 0.1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09

Setting: shared_type, thin = 0.5

thin <- 0.5
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09

Setting: shared_type, thin = 1

thin <- 1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Version Author Date
bda6e43 XSun 2025-04-09

aFib-ebi-a-GCST006414

Setting: shared_all, thin = 0.1

trait <- "aFib-ebi-a-GCST006414"
thin <- 0.1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Version Author Date
bda6e43 XSun 2025-04-09

Setting: shared_all, thin = 0.5

thin <- 0.5
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Version Author Date
bda6e43 XSun 2025-04-09

Setting: shared_all, thin = 1

thin <- 1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Version Author Date
bda6e43 XSun 2025-04-09

Setting: shared_type, thin = 0.1

thin <- 0.1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Version Author Date
bda6e43 XSun 2025-04-09

Setting: shared_type, thin = 0.5

thin <- 0.5
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Version Author Date
bda6e43 XSun 2025-04-09

Setting: shared_type, thin = 1

thin <- 1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Version Author Date
bda6e43 XSun 2025-04-09

SCZ-ieu-b-5102

Setting: shared_all, thin = 0.1

trait <- "SCZ-ieu-b-5102"
thin <- 0.1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Version Author Date
bda6e43 XSun 2025-04-09

Setting: shared_all, thin = 0.5

thin <- 0.5
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Version Author Date
bda6e43 XSun 2025-04-09

Setting: shared_all, thin = 1

thin <- 1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Version Author Date
bda6e43 XSun 2025-04-09

Setting: shared_type, thin = 0.1

thin <- 0.1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Version Author Date
bda6e43 XSun 2025-04-09

Setting: shared_type, thin = 0.5

thin <- 0.5
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Version Author Date
bda6e43 XSun 2025-04-09

Setting: shared_type, thin = 1

thin <- 1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Version Author Date
bda6e43 XSun 2025-04-09 

sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] forcats_0.5.1    stringr_1.5.1    dplyr_1.1.4      purrr_1.0.2     
 [5] readr_2.1.2      tidyr_1.3.0      tibble_3.2.1     tidyverse_1.3.1 
 [9] ggplot2_3.5.1    ctwas_0.5.4.9000

loaded via a namespace (and not attached):
  [1] readxl_1.4.0                backports_1.4.1            
  [3] workflowr_1.7.0             BiocFileCache_2.4.0        
  [5] repr_1.1.4                  lazyeval_0.2.2             
  [7] BiocParallel_1.30.3         GenomeInfoDb_1.39.9        
  [9] LDlinkR_1.2.3               digest_0.6.29              
 [11] ensembldb_2.20.2            htmltools_0.5.2            
 [13] fansi_1.0.3                 magrittr_2.0.3             
 [15] memoise_2.0.1               tzdb_0.4.0                 
 [17] Biostrings_2.64.0           modelr_0.1.8               
 [19] AMR_2.1.1                   matrixStats_0.62.0         
 [21] locuszoomr_0.2.1            prettyunits_1.1.1          
 [23] colorspace_2.0-3            skimr_2.1.4                
 [25] blob_1.2.3                  rvest_1.0.2                
 [27] rappdirs_0.3.3              ggrepel_0.9.1              
 [29] haven_2.5.0                 xfun_0.41                  
 [31] crayon_1.5.1                RCurl_1.98-1.7             
 [33] jsonlite_1.8.0              zoo_1.8-10                 
 [35] glue_1.6.2                  gtable_0.3.0               
 [37] zlibbioc_1.42.0             XVector_0.36.0             
 [39] DelayedArray_0.22.0         BiocGenerics_0.42.0        
 [41] scales_1.3.0                DBI_1.2.2                  
 [43] Rcpp_1.0.12                 viridisLite_0.4.0          
 [45] progress_1.2.2              bit_4.0.4                  
 [47] stats4_4.2.0                htmlwidgets_1.5.4          
 [49] httr_1.4.3                  ellipsis_0.3.2             
 [51] pkgconfig_2.0.3             XML_3.99-0.14              
 [53] farver_2.1.0                sass_0.4.1                 
 [55] dbplyr_2.1.1                utf8_1.2.2                 
 [57] tidyselect_1.2.0            labeling_0.4.2             
 [59] rlang_1.1.2                 later_1.3.0                
 [61] AnnotationDbi_1.58.0        munsell_0.5.0              
 [63] pgenlibr_0.3.3              cellranger_1.1.0           
 [65] tools_4.2.0                 cachem_1.0.6               
 [67] cli_3.6.1                   generics_0.1.2             
 [69] RSQLite_2.3.1               broom_0.8.0                
 [71] evaluate_0.15               fastmap_1.1.0              
 [73] yaml_2.3.5                  knitr_1.39                 
 [75] bit64_4.0.5                 fs_1.5.2                   
 [77] KEGGREST_1.36.3             AnnotationFilter_1.20.0    
 [79] whisker_0.4                 xml2_1.3.3                 
 [81] biomaRt_2.54.1              compiler_4.2.0             
 [83] rstudioapi_0.13             plotly_4.10.0              
 [85] filelock_1.0.2              curl_4.3.2                 
 [87] png_0.1-7                   reprex_2.0.1               
 [89] bslib_0.3.1                 stringi_1.7.6              
 [91] highr_0.9                   GenomicFeatures_1.48.3     
 [93] lattice_0.20-45             ProtGenerics_1.28.0        
 [95] Matrix_1.5-3                vctrs_0.6.5                
 [97] pillar_1.9.0                lifecycle_1.0.4            
 [99] jquerylib_0.1.4             data.table_1.14.2          
[101] cowplot_1.1.1               bitops_1.0-7               
[103] irlba_2.3.5                 httpuv_1.6.5               
[105] rtracklayer_1.56.0          GenomicRanges_1.48.0       
[107] R6_2.5.1                    BiocIO_1.6.0               
[109] promises_1.2.0.1            gridExtra_2.3              
[111] IRanges_2.30.0              codetools_0.2-18           
[113] assertthat_0.2.1            SummarizedExperiment_1.26.1
[115] rprojroot_2.0.3             rjson_0.2.21               
[117] withr_2.5.0                 GenomicAlignments_1.32.0   
[119] Rsamtools_2.12.0            S4Vectors_0.34.0           
[121] GenomeInfoDbData_1.2.8      parallel_4.2.0             
[123] hms_1.1.1                   grid_4.2.0                 
[125] gggrid_0.2-0                rmarkdown_2.25             
[127] MatrixGenerics_1.8.0        logging_0.10-108           
[129] git2r_0.30.1                mixsqp_0.3-43              
[131] Biobase_2.56.0              lubridate_1.8.0            
[133] base64enc_0.1-3             restfulr_0.0.14