R/Key2KEGGEnrich.R

In ppdragondw/Key2Enrich: R package of gene set enrichment analysis

#' Get enrichment output matrix of enriched KEGG pathway
#'
#' @param inputSample input formatted sample
#' @param inputSpecies human, mouse, rat
#' @param adjustMethod p.adjust.methods,
#' c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")
#' @param filterMethod pValue or other character vector
#' @param filterValue must by numeric, value from 0 to 1
#' @return data in dataframe class with pValue, adjust pValue of significate KEGG pathway
#' @export
#' @importFrom stats p.adjust
#' @examples
#' data(inputSample)
#' inputSample<-as.data.frame(inputSample)
#' \dontrun{
#' thisKEGGEnricherMatrix<-KEGGEnricherMatrixRealTime(inputSample,"mouse","fdr","fdr",0.05)
#' }

KEGGEnricherMatrixRealTime<-function(inputSample,
                                     inputSpecies,
                                     adjustMethod,
                                     filterMethod,
                                     filterValue)
  {
  KEGGSpecies<-speciesKEGGConvert(inputSpecies)
  allGeneInPathwayDF<-getAllGeneInPathwayDF(KEGGSpecies)

  N<-getN(allGeneInPathwayDF)
  n<-get_n(inputSample,allGeneInPathwayDF)
  pvalueMatrix<-apply(getTotalPathNames(KEGGSpecies),
                    1,
                    getPValue,
                    thisKEGGSpecies=KEGGSpecies,
                    thisInputSampleKEGG=inputSample,
                    N=N,
                    n=n)

  pvalueDF<-data.frame(pathID=unlist(sapply(pvalueMatrix,"[",1))
                     ,M=unlist(sapply(pvalueMatrix,"[",2))
                     ,m=unlist(sapply(pvalueMatrix,"[",3))
                     ,N=unlist(sapply(pvalueMatrix,"[",4))
                     ,n=unlist(sapply(pvalueMatrix,"[",5))
                     ,pValue=unlist(sapply(pvalueMatrix,"[",6))
                     ,KEGGGenes=unlist(sapply(pvalueMatrix,"[",7))
                     ,entrezGenes=unlist(sapply(pvalueMatrix,"[",8))
                     ,genes=unlist(sapply(pvalueMatrix,"[",9))
                     ,ensemblGenes=unlist(sapply(pvalueMatrix,"[",10)))

pvalueDF$adjpValue<-p.adjust(pvalueDF$pValue,method = adjustMethod)
filterValueDF<-NULL
if (filterMethod=="pValue"){
  filterValueDF<-pvalueDF[pvalueDF$pValue<filterValue,]
  filterValueDF$negativeLog<- -log10(filterValueDF$pValue)
}
else
{
  filterValueDF<-pvalueDF[pvalueDF$adjpValue<filterValue,]
  filterValueDF$negativeLog<- -log10(filterValueDF$adjpValue)
}
allPathNameAndID<-getAllPathNameAndID(KEGGSpecies)
filterValuePathNameDF<-
  merge(filterValueDF,allPathNameAndID,by.x="pathID",by.y="pathID")
filterValuePathNameDF <-
  filterValuePathNameDF[order(filterValuePathNameDF$negativeLog),]
filterValuePathNameDF<-
  filterValuePathNameDF[filterValuePathNameDF$pathID!="mmu01100",]
return (filterValuePathNameDF)
}

#' Performe enrichment analysis based on KEGG pathway,
#' plot barplot of significantly enriched KEGG pathway,
#' mapping genes on KEGG pathway image
#'
#' @param inputSample input formatted sample
#' @param inputSpecies human, mouse, rat
#' @param adjustMethod p.adjust.methods,
#' c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")
#' @param filterMethod pValue or other character vector
#' @param filterValue must by numeric, value from 0 to 1
#' @param ifbarplot barplot or not, TRUE/FALSE
#' @param ifMapOnPath pathway mapping or not, TRUE/FALSE
#' @param type KEGG, Reactome, BP,MF,CC
#' @param imgWidth the width of export file
#' @param imgHeight the height of export file
#' @return data in dataframe class with pValue, adjust pValue of significate KEGG pathway
#' @export
#' @examples
#' data(inputSample)
#' inputSample<-as.data.frame(inputSample)
#' head(inputSample)
#' \dontrun{
#' KEGGSigMx<-Key2KEGGEnrich(inputSample,"mouse","fdr","fdr",0.05,TRUE,TRUE,"KEGG",15,20)
#' }

Key2KEGGEnrich<-function (inputSample,
                          inputSpecies,
                          adjustMethod,
                          filterMethod,
                          filterValue,
                          ifbarplot,
                          ifMapOnPath,
                          type,
                          imgWidth,
                          imgHeight){
  mx<-KEGGEnricherMatrixRealTime(inputSample,
                                 inputSpecies,
                                 adjustMethod,
                                 filterMethod,
                                 filterValue)
  if (ifbarplot) {Key2EnrichBarplot(mx,type,imgWidth,imgHeight)}
  if (ifMapOnPath) {o<-apply(mx,1,plotSigImg,inputSample=inputSample,inputSpecies=inputSpecies)}
  return (mx)
}

#' Download KEGG pathway files and mapping genes on pathway
#'
#' @param plotPathID KEGG pathway ID
#' @param inputSampleKEGG input formatted sample
#' @param inputSpecies human, mouse, rat
#' @return NA
#' @export
#' @examples
#' data(inputSample)
#' inputSample<-as.data.frame(inputSample)
#' head(inputSample)
#' \dontrun{
#' mappingOnSpecifiedKEGGPathway("mmu05160",inputSample,"mouse")
#' }

mappingOnSpecifiedKEGGPathway<-function (plotPathID,inputSampleKEGG,inputSpecies){
  #plotPathID:specific KEGG pathway ID
  o<-plotSigImg(plotPathID,inputSampleKEGG,inputSpecies)
}