Description Usage Arguments Details Value Examples
View source: R/GSEA_report_MS.R
In order fo the results of GSEA to be more comprehensive, we make a function to summarize the results
1 2 | GSEA_report_MS(GSEA_result, GeneSetAnnot=F ,GeneSets_annot=NULL, TabCols=NULL,
GeneStats_annot=NULL, StatsCols=NULL, GSEA_Dir)
|
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 |
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.
data.frame ofject
1 2 3 4 5 6 | 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"))
}
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