GSEA_report_MS: Function to make a GSEA summary table with Mouse gene symbol...

In machalen/AnalysisFunctions: Package with basic analysis functions for genomic data

Description

In order fo the results of GSEA to be more comprehensive, we make a function to summarize the results

Usage

GSEA_report_MS(GSEA_result, GeneSetAnnot=F ,GeneSets_annot=NULL, TabCols=NULL, 
                             GeneStats_annot=NULL, StatsCols=NULL, GSEA_Dir)

Arguments

GSEA_result	Directory path with results of one GSEA analysis
GeneSetAnnot	TRUE When gene sets are described in a table and we want them to be included
GeneSets_annot	Table with gene sets annotation and rownames(GeneSets_annot) == gene set name
TabCols	Columns of the GeneSets_annot to be included
GeneStats_annot	Table with the statistics of genes and rownames == Genesymbol
StatsCols	Columns of the table GeneStats_annot to be included
GSEA_Dir	Directory to save the results

Details

This function makes a summary of the GSEA results with the different sub-folders. The output .csv contains all gene sets in the top (selected by the user) together with the genes in each case.

Value

data.frame ofject

Examples

for (i in 1:length(inDirFiles)) {
  GSEA_result <- file.path(GSEA_Dir, inDirFiles[i])
  GSEA_report_MS(GSEA_result=GSEA_result, GeneSetAnnot=T ,GeneSets_annot=GSEA_info, 
                   TabCols=c("source","descriptionBrief","descriptionFull", "nGenes"))
  
}

machalen/AnalysisFunctions documentation built on Nov. 11, 2019, 10:26 a.m.