Last updated: 2024-10-17
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Knit directory: multigroup_ctwas_analysis/
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We do enrichment analysis for the results here: https://sq-96.github.io/multigroup_ctwas_analysis/multi_group_6traits_15weights_ess.html
The model is:
glm(PIP ~ gene set membership, family = quasibinomial('logit')).
We do this regression for one gene set at a time.
The PIP vector contains:
0.5*min(gene pip within credible set)We assign 1 to the genes with PIP > 0.5/0.8 & in cs and 0 for others. We name this vector as binarized_PIP. We test the association between the binarized_PIP and geneset_membership.
The testing matrix is:
| geneset_membership | 0 | 1 |
|---|---|---|
| binarized_pip 0 | a | b |
| binarized_pip 1 | c | d |
Where:
a is the count where binarized_pip = 0 and
geneset_membership = 0.b is the count where binarized_pip = 0 and
geneset_membership = 1.c is the count where binarized_pip = 1 and
geneset_membership = 0.d is the count where binarized_pip = 1 and
geneset_membership = 1.| aFib | LDL | IBD | SBP | SCZ | WBC | ||
|---|---|---|---|---|---|---|---|
| Non-redundant Go | gobp | 18 | 10 | 18 | 1 | 2 | 11 |
| gocc | 7 | 14 | 1 | 0 | 0 | 4 | |
| gomf | 2 | 3 | 3 | 0 | 0 | 0 | |
| Fractional model | gobp | 5806 | 4497 | 5122 | 3757 | 4291 | 1701 |
| gocc | 671 | 582 | 613 | 461 | 506 | 200 | |
| gomf | 2148 | 1174 | 2144 | 1578 | 1800 | 699 | |
| Fisher exact | gobp - pip0.5 | 32 | 29 | 0 | 0 | 0 | 39 |
| gocc - pip0.5 | 16 | 17 | 0 | 0 | 0 | 0 | |
| gomf - pip0.5 | 0 | 0 | 0 | 0 | 0 | 0 | |
| gobp - pip0.8 | 3 | 22 | 1 | 0 | 0 | 3 | |
| gocc - pip0.8 | 1 | 23 | 0 | 0 | 0 | 0 | |
| gomf - pip0.8 | 0 | 2 | 0 | 0 | 0 | 0 |
| pathway | ||
|---|---|---|
| aFib | gobp | cardiac conduction |
| cell communication involved in cardiac conduction | ||
| cardiac muscle contraction | ||
| regulation of heart rate | ||
| cardiac muscle cell action potential | ||
| regulation of cardiac muscle contraction | ||
| cell-cell signaling involved in cardiac conduction | ||
| regulation of heart rate by cardiac conduction | ||
| heart contraction | ||
| heart process | ||
| gocc | sarcolemma | |
| contractile fiber | ||
| myofibril | ||
| sarcoplasm | ||
| sarcomere | ||
| Z disc | ||
| I band | ||
| cell junction | ||
| gomf | / | |
| LDL | gobp | Cholesterol Transport |
| Lipoprotein Metabolic Process | ||
| Lipid Metabolic Process | ||
| Regulation of Plasma Lipoprotein Particle Levels | ||
| Triglyceride Metabolic Process | ||
| Cholesterol Biosynthetic Process | ||
| gocc | endoplasmic reticulum | |
| endocytic vesicle | ||
| clathrin-coated endocytic vesicle membrane | ||
| protein-lipid complex | ||
| plasma lipoprotein particle | ||
| lipoprotein particle | ||
| high-density lipoprotein particle | ||
| endosome membrane | ||
| COPII-coated ER to Golgi transport vesicle | ||
| gomf | / | |
| IBD | gobp | / |
| gocc | / | |
| gomf | / | |
| SBP | gobp | / |
| gocc | / | |
| gomf | / | |
| SCZ | gobp | / |
| gocc | / | |
| gomf | / | |
| WBC | gobp | leukocyte activation |
| immune system process | ||
| myeloid leukocyte activation | ||
| myeloid leukocyte migration | ||
| leukocyte activation involved in immune response | ||
| leukocyte mediated immunity | ||
| neutrophil mediated immunity | ||
| neutrophil activation | ||
| leukocyte degranulation | ||
| granulocyte migration | ||
| granulocyte activation | ||
| immune effector process | ||
| neutrophil activation involved in immune response | ||
| neutrophil degranulation | ||
| leukocyte migration | ||
| gocc | / | |
| gomf | / |
| pathway | ||
|---|---|---|
| aFib | gobp | sarcomere organization |
| gocc | / | |
| gomf | / | |
| LDL | gobp | triglyceride metabolic process |
| cholesterol transport | ||
| sterol transport | ||
| plasma lipoprotein particle clearance | ||
| regulation of plasma lipoprotein particle levels | ||
| receptor-mediated endocytosis | ||
| low-density lipoprotein particle remodeling | ||
| lipoprotein metabolic process | ||
| gocc | LDL particle structure and composition | |
| LDL receptor-mediated endocytosis | ||
| Intracellular processing of LDL | ||
| Regulation of LDL receptor levels | ||
| Synthesis and secretion of lipoproteins | ||
| gomf | / | |
| IBD | gobp | cellular response to cytokine stimulus |
| gocc | / | |
| gomf | / | |
| SBP | gobp | / |
| gocc | / | |
| gomf | / | |
| SCZ | gobp | / |
| gocc | / | |
| gomf | / | |
| WBC | gobp | / |
| gocc | / | |
| gomf | / |
trait <- "aFib-ebi-a-GCST006414"
file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Biological_Process_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Cellular_Component_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Molecular_Function_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 5806"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 671"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 2148"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 32"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 16"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 3"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 1"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}trait <- "LDL-ukb-d-30780_irnt"
file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Biological_Process_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Cellular_Component_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Molecular_Function_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 4497"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 582"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 1774"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 29"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 17"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 22"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 23"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 2"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}trait <- "IBD-ebi-a-GCST004131"
file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Biological_Process_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Cellular_Component_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Molecular_Function_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 5122"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 613"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 2144"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 1"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}trait <- "SBP-ukb-a-360"
file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Biological_Process_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Cellular_Component_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}[1] "No enriched Go terms"file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Molecular_Function_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}[1] "No enriched Go terms"load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 3757"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 461"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 1578"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}trait <- "SCZ-ieu-b-5102"
file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Biological_Process_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Cellular_Component_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}[1] "No enriched Go terms"file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Molecular_Function_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}[1] "No enriched Go terms"load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 4291"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 506"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 1800"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}trait <- "WBC-ieu-b-30"
file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Biological_Process_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Cellular_Component_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}file <- paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_nonredundant_",trait,"_GO_Molecular_Function_2021.rdata")
if(file.exists(file)) {
load(file)
db_enrichment <- db_enrichment[db_enrichment$Adjusted.P.value < 0.05,]
if(nrow(db_enrichment) > 0) {
db_enrichment <- db_enrichment[,c("Term","Overlap","Adjusted.P.value","Genes")]
DT::datatable(db_enrichment,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO biological process'),options = list(pageLength = 10) )
}else{
print("No enriched Go terms")
}
}else{
print("No enriched Go terms")
}[1] "No enriched Go terms"load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 1701"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 200"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 699"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 39"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip05_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gobp.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 16069"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 3"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gocc.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 2022"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}load(paste0("/project/xinhe/xsun/multi_group_ctwas/11.multi_group_1008/postprocess/enrichment_fisher_pip08_", trait, "_gomf.rdata"))
sprintf("the number of pathways included: %s", nrow(summary))[1] "the number of pathways included: 4674"sprintf("the number of pathways with FDR <0.05 : %s", nrow(summary[summary$fdr < 0.05,]))[1] "the number of pathways with FDR <0.05 : 0"summary <- summary[order(summary$fdr, decreasing = F),]
if(nrow(summary[summary$fdr < 0.05,]) >= 1) {
summary <- summary[1:nrow(summary[summary$fdr < 0.05,]),]
DT::datatable(summary,caption = htmltools::tags$caption( style = 'caption-side: topleft; text-align = left; color:black;','Enrichment results for GO molecular function , pathways with FDR < 0.05 are shown'),options = list(pageLength = 10) )
}
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
loaded via a namespace (and not attached):
[1] Rcpp_1.0.12 rstudioapi_0.13 knitr_1.39 magrittr_2.0.3
[5] workflowr_1.7.0 R6_2.5.1 rlang_1.1.2 fastmap_1.1.0
[9] fansi_1.0.3 stringr_1.5.1 tools_4.2.0 DT_0.22
[13] xfun_0.41 utf8_1.2.2 cli_3.6.1 git2r_0.30.1
[17] jquerylib_0.1.4 crosstalk_1.2.0 htmltools_0.5.2 rprojroot_2.0.3
[21] yaml_2.3.5 digest_0.6.29 tibble_3.2.1 lifecycle_1.0.4
[25] later_1.3.0 htmlwidgets_1.5.4 sass_0.4.1 vctrs_0.6.5
[29] promises_1.2.0.1 fs_1.5.2 glue_1.6.2 evaluate_0.15
[33] rmarkdown_2.25 stringi_1.7.6 bslib_0.3.1 compiler_4.2.0
[37] pillar_1.9.0 jsonlite_1.8.0 httpuv_1.6.5 pkgconfig_2.0.3