FUN_GSEA_ForOFFL.R

## Build files for GSEA official input

FUN_GSEA_ForOFFL = function(GeneExp.df,
                            Group1 = Group1.set, Group2 = Group2.set,
                            Group1Name = Group1_Name,Group2Name = Group2_Name,
                            SavePath = SavePath, ExportName = ExportName,
                            AnnoName = "AvB"
){

##### Build Expression matrix for GSEA #####
  GeneExp_GSEA.df <- cbind(
    NAME=row.names(GeneExp.df),
    Description = rep("na", nrow(GeneExp.df)),
    GeneExp.df[,c(Group1, Group2)]
  )

  GSEA_SampleCol.df <- data.frame(t(colnames(GeneExp_GSEA.df)), stringsAsFactors=FALSE)
  colnames(GSEA_SampleCol.df) <- GSEA_SampleCol.df

  GeneExp_GSEA.df <- rbind(GSEA_SampleCol.df,GeneExp_GSEA.df)

  GeneExp_GSEA.df <- data.frame(
    "NAME" = c("#1.2",nrow(GeneExp.df)),
    "Description" = c('',length(c(Group1, Group2)))
  ) %>%
    rbind.fill(GeneExp_GSEA.df)
  rm(GSEA_SampleCol.df)

##### Build Group Files #####
  ## Set the group array
  Pheno_sum.df <- c(ncol(GeneExp_GSEA.df)-2,2,1) %>% t() %>% data.frame() %>%
    rbind.fill(c(paste0("#",Group1Name),paste0(Group2Name)) %>% t() %>% data.frame(stringsAsFactors=FALSE)) %>%
    rbind.fill(c(rep(0,length(Group1)),rep(1,length(Group2))) %>% t() %>% data.frame())


##### Export Result #####
  write.table(
    GeneExp_GSEA.df,
    file=paste0(SavePath,"/OFFL_GSEA_",ExportName,AnnoName,"_collapsed.gct"),
    quote = FALSE,row.names = FALSE,col.names = FALSE, na = "",sep = '\t'
  )
  write.table(
    Pheno_sum.df,
    file=paste0(SavePath,"/OFFL_GSEA_",ExportName,AnnoName,".cls"),
    quote = FALSE,row.names = FALSE, na = "",col.names = FALSE
  )


}