#Magda Arnal
#02/07/2019
#Function to make the report by gene, Getting the output of the other report make functions
############################################################################################################################
##################################REPORT SUMMARY FOR EACH GENE##############################################################
GSEA_genes_Report <- function(GSEA_summary, name.f, symbol.col="SYMBOL", GSEA_Dir=GSEADir) {
#GSEA_summary: csv amb el summary dels resultats de GSEA generat amb la funció GSEA_report_Make
#name.f: name of the output file
#symbol.col: Columna que conté els gene symbols
symb <- unique(GSEA_summary[,symbol.col])
nTimes <- vector()
GeneSets <- vector()
symbols <- vector()
description <- vector()
pval <- vector()
padj <- vector()
log2FC <- vector()
for (s in symb) {
tab_symb <- GSEA_summary[GSEA_summary[,symbol.col] == s,]
nTimes <- c(nTimes, nrow(tab_symb))
GeneSets <- c(GeneSets, paste(unique(tab_symb$GENE_SET), collapse="//"))
description <- c(description, paste(unique(tab_symb$GENENAME), collapse="//"))
pval <- c(pval, tab_symb[1,grep("P.Value", colnames(tab_symb))])
padj <- c(padj, tab_symb[1,grep("adj.P.Val", colnames(tab_symb))])
log2FC <- c(log2FC, tab_symb[1,grep("logFC", colnames(tab_symb))])
}
gene.df <- data.frame(symb, description, nTimes, GeneSets, pval, padj, log2FC)
#gene.df <- gene.df[order(gene.df$pval),]
gene.df <- gene.df[order(gene.df$nTimes, decreasing = T),]
write.csv2(gene.df, file=file.path(GSEA_Dir, paste(name.f, "_GenesEnriched",".csv", sep="")), row.names=F)
}
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