Merge DiffBind and Uropa outputs with the attached functions

[tovahmarkowitz]

prepDiffBind <- function(DiffBindFile) {
  inDiffBindData <- read.delim(DiffBindFile)
  DiffBindData <- inDiffBindData[order(inDiffBindData$seqnames,inDiffBindData$start),]
  DiffBindData$peak_id <- paste0("Peak",1:nrow(DiffBindData))
  return(DiffBindData)
}

loadAndMerge <- function(DiffBindFile, UropaFile) {
  DiffBindData <- prepDiffBind(DiffBindFile)
  UropaData <- read.delim(UropaFile)
  MergedData <- merge(DiffBindData,UropaData)

  #which(MergedData$end != MergedData$peak_end)
  #names(MergedData)
  #[1] "peak_id"           "seqnames"          "start"             "end"              
  #[5] "width"             "strand"            "Conc"              "Conc_D5pos4"      
  #[9] "Conc_D5neg4"       "Fold"              "p.value"           "FDR"              
  #[13] "Called1"           "Called2"           "peak_chr"          "peak_start"       
  #[17] "peak_end"          "peak_score"        "peak_strand"       "feature"          
  #[21] "feat_start"        "feat_end"          "feat_strand"       "feat_anchor"      
  #[25] "distance"          "relative_location" "feat_ovl_peak"     "peak_ovl_feat"    
  #[29] "gene_id"           "gene_name"         "gene_type"         "name"

  MergedData2 <- MergedData[order(MergedData$FDR,decreasing = F),
                            c(2:5,1,8:10,12,21:26,29:32)]
  return(MergedData2)
}

FilterMerged <- function(MergedData2,FDRcutoff=0.05,FoldCutoff=0) {
  MergedDataFDR <- MergedData2[which(MergedData2$FDR < FDRcutoff),]
  MergedDataFiltered <- MergedDataFDR[which((MergedDataFDR$Fold > FoldCutoff) | 
                                            (MergedDataFDR$Fold) < -(FoldCutoff)),]
  return(MergedDataFiltered)
}