Last updated: 2024-01-11

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Knit directory: multigroup_ctwas_analysis/

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Rmd 21f7647 XSun 2024-01-09 update
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Overview

We performed gene set enrichment analysis for the genes with susie pip > 0.8 using logistic susie(https://karltayeb.github.io/logistic-susie-gsea/index.html) and susie.

Logistic Susie

We binarize the response variable Y based on our selected gene list(genes with susie pip>0.8 from multi-tissue ctwas analysis). Y is a n*1 vector (n=#of genes)

The explanatory variable X indicate if the gene is part of a specific pathway. X is a n*m matrix, n=#of genes, m=# of pathways

Susie

The response variable Y is the outcome of MAGMA (z-scores of the genes with susie pip > 0.8).

The explanatory variable X is the same with logistic susie

Pathways

The pathways are from Go Biological Process (gobp), Go Molecular Function (gomf), Go Cellular Component (gocc) and KEGG.

Functions

library(gseasusie)
library(tidyverse)
create_pip_datatable <- function(linear_fit) {
  pip <- linear_fit$pip
  pip <- as.data.frame(cbind(names(pip), pip))
  rownames(pip) <- seq(1, nrow(pip), by = 1)
  pip <- pip[order(as.numeric(pip$pip), decreasing = TRUE), ]
  colnames(pip) <- c("pwy", "PIP")

  DT::datatable(pip, 
                caption = htmltools::tags$caption(style = 'caption-side: left; text-align: left; color:black; font-size:150%;', 
                                                  'Susie PIPs'), 
                options = list(pageLength = 10))
}

aFib

Go Biological Process

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/aFib-ebi-a-GCST006414_cutoff08_gobp.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

Go Molecular Function

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/aFib-ebi-a-GCST006414_cutoff08_gocc.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

Cellular Component

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/aFib-ebi-a-GCST006414_cutoff08_gocc.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

KEGG

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/aFib-ebi-a-GCST006414_cutoff08_kegg.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

IBD

Go Biological Process

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/IBD-ebi-a-GCST004131_cutoff08_gobp.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

Go Molecular Function

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/IBD-ebi-a-GCST004131_cutoff08_gocc.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

Cellular Component

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/IBD-ebi-a-GCST004131_cutoff08_gocc.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

KEGG

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/IBD-ebi-a-GCST004131_cutoff08_kegg.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

LDL

Go Biological Process

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/LDL-ukb-d-30780_irnt_cutoff08_gobp.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

Go Molecular Function

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/LDL-ukb-d-30780_irnt_cutoff08_gocc.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

Cellular Component

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/LDL-ukb-d-30780_irnt_cutoff08_gocc.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

KEGG

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/LDL-ukb-d-30780_irnt_cutoff08_kegg.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

SBP

Go Biological Process

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/SBP-ukb-a-360_cutoff08_gobp.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

Go Molecular Function

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/SBP-ukb-a-360_cutoff08_gocc.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

Cellular Component

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/SBP-ukb-a-360_cutoff08_gocc.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

KEGG

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/SBP-ukb-a-360_cutoff08_kegg.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

SCZ

Go Biological Process

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/SCZ-ieu-b-5102_cutoff08_gobp.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

Go Molecular Function

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/SCZ-ieu-b-5102_cutoff08_gocc.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

Cellular Component

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/SCZ-ieu-b-5102_cutoff08_gocc.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

KEGG

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/SCZ-ieu-b-5102_cutoff08_kegg.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

WBC

Go Biological Process

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/WBC-ieu-b-30_cutoff08_gobp.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

Go Molecular Function

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/WBC-ieu-b-30_cutoff08_gocc.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

Cellular Component

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/WBC-ieu-b-30_cutoff08_gocc.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

KEGG

Logistice Susie

load("/project/xinhe/xsun/ctwas/4.multi_tissue_process/results/susie_old/WBC-ieu-b-30_cutoff08_kegg.rdata")
gseasusie::enrichment_volcano(logistic.fit, ora)

Version Author Date
a5f7fb7 XSun 2024-01-09 
gseasusie::interactive_table(logistic.fit, ora)

Susie

create_pip_datatable(linear_fit = linear.fit.subset)

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         
 [4] purrr_1.0.2          readr_2.1.2          tidyr_1.3.0         
 [7] tibble_3.2.1         ggplot2_3.3.5        tidyverse_1.3.1     
[10] gseasusie_0.0.0.9000

loaded via a namespace (and not attached):
 [1] httr_1.4.3           sass_0.4.1           jsonlite_1.8.0      
 [4] modelr_0.1.8         bslib_0.3.1          assertthat_0.2.1    
 [7] highr_0.9            cellranger_1.1.0     yaml_2.3.5          
[10] pillar_1.9.0         backports_1.4.1      lattice_0.20-45     
[13] glue_1.6.2           digest_0.6.29        promises_1.2.0.1    
[16] rvest_1.0.2          colorspace_2.0-3     htmltools_0.5.2     
[19] httpuv_1.6.5         Matrix_1.5-3         reactR_0.5.0        
[22] pkgconfig_2.0.3      broom_0.8.0          VEB.Boost_0.0.0.9039
[25] haven_2.5.0          mvtnorm_1.1-3        scales_1.2.0        
[28] whisker_0.4          later_1.3.0          spatstat.utils_3.0-1
[31] tzdb_0.4.0           git2r_0.30.1         generics_0.1.2      
[34] farver_2.1.0         DT_0.22              ellipsis_0.3.2      
[37] withr_2.5.0          cli_3.6.1            magrittr_2.0.3      
[40] crayon_1.5.1         readxl_1.4.0         evaluate_0.15       
[43] reactable_0.4.4      data.tree_1.0.0      fs_1.5.2            
[46] fansi_1.0.3          xml2_1.3.3           mr.ash.alpha_0.1-42 
[49] tools_4.2.0          hms_1.1.1            lifecycle_1.0.4     
[52] matrixStats_0.62.0   munsell_0.5.0        reprex_2.0.1        
[55] compiler_4.2.0       jquerylib_0.1.4      rlang_1.1.2         
[58] grid_4.2.0           rstudioapi_0.13      htmlwidgets_1.5.4   
[61] crosstalk_1.2.0      labeling_0.4.2       rmarkdown_2.14      
[64] gtable_0.3.0         DBI_1.1.2            R6_2.5.1            
[67] lubridate_1.8.0      knitr_1.39           emulator_1.2-21     
[70] fastmap_1.1.0        utf8_1.2.2           workflowr_1.7.0     
[73] rprojroot_2.0.3      stringi_1.7.6        parallel_4.2.0      
[76] Rcpp_1.0.8.3         vctrs_0.6.5          dbplyr_2.1.1        
[79] tidyselect_1.2.0     xfun_0.30