R/input.R

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

#' Read samples files with different annotation ID
#'
#' @param fileName input file in csv format
#' @param IDColumn must be numberic,the column number of sample ID
#' @param logFCColumn must be numberic,
#' the column number of sample log fold change
#' @param IDType Human: entrezgene, hgnc_symbol, ensembl_gene_id,
#' Mouse: entrezgene, mgi_symbol, ensembl_gene_id,
#' Rat: entrezgene, rgd_symbol, ensembl_gene_id
#' @return Sample file in data.frame format
#' @export
#' @importFrom utils read.csv
#' @examples
#' path<-system.file(package = "Key2Enrich")
#' filePath<-paste(path,"/extdata",sep="")
#' file<-paste(filePath,sep="","/sampleFile.csv")
#' entrezgene_sample<-readInputFile(file,IDColumn=1,
#'                                  logFCColumn=2,IDType="mgi_symbol")
#' head(entrezgene_sample)

readInputFile<-function (fileName,IDColumn,logFCColumn,IDType){
inputSample<-read.csv(fileName)
sample<-subset(inputSample,select=-c(IDColumn,logFCColumn))

sample$ID<-inputSample[,IDColumn]
sample$log2FC<-inputSample[,logFCColumn]

colnames(sample)[which(names(sample)=="ID")]<-IDType

return (sample)
}

#' Format input file to dataframe class with entrez ID, symbol and ensembl ID
#'
#' @param filename input file in csv format
#' @param IDColumn must be numberic,the column number of sample ID
#' @param logFCColumn must be numberic,
#' the column number of sample log fold change
#' @param IDType Human: entrezgene, hgnc_symbol, ensembl_gene_id,
#' Mouse: entrezgene, mgi_symbol, ensembl_gene_id,
#' Rat: entrezgene, rgd_symbol, ensembl_gene_id
#' @param inputSpecies human, mouse, rat
#' @return input sample in dataframe class with entrez ID, symbol and ensembl ID
#' @export
#' @examples
#' path<-system.file(package = "Key2Enrich")
#' filePath<-paste(path,"/extdata",sep="")
#' file<-paste(filePath,sep="","/sampleFile.csv")
#' \donttest{
#' inputSample<-formatInputSample(file,
#'                                IDColumn=1,
#'                                logFCColumn=2,
#'                                "mgi_symbol",
#'                                "mouse")
#'                                }
formatInputSample<-function (filename,
                               IDColumn,
                               logFCColumn,
                               IDType,
                               inputSpecies){
    sample<-readInputFile(filename,IDColumn,logFCColumn,IDType)
    IDColValue<-sample[,(names(sample)==IDType)]
    IDMapping<-getAllTypesID(inputSpecies,IDType,IDColValue)
    inputSampleWith3IDs<-merge(sample,
                             IDMapping,
                             by.x=IDType,
                             by.y=IDType)
    KEGGSpecies<-speciesKEGGConvert(inputSpecies)
    inputSampleKEGG<-merge(inputSampleWith3IDs,
                         KEGGID2EntrezID(KEGGSpecies),
                         by.x="entrezgene",
                         by.y="entrezgene")
    return (inputSampleKEGG)
}

#' Convert input species to biomart species
#'
#' @param inputSpecies human, mouse, rat
#' @return species of biomart format,
#' human:hsapiens_gene_ensembl,
#' mouse:mmusculus_gene_ensembl,
#' rat:rnorvegicus_gene_ensembl
#'
speciesConvert2Biomart <- function(inputSpecies) {
    switch(inputSpecies,
         mouse = "mmusculus_gene_ensembl",
         human = "hsapiens_gene_ensembl",
         rat = "rnorvegicus_gene_ensembl")
}

#' Convert input species to KEGG species
#'
#' @param inputSpecies human, mouse, rat
#' @return species of KEGG format, human:hsa, mouse:mmu, rat:rno
#'
speciesKEGGConvert <- function(inputSpecies) {
switch(inputSpecies,
         mouse = "mmu",
         human = "hsa",
         rat = "rno")
}
#' Get gene symbol from different species
#'
#' @param thisKEGGSpecies species in KEGG format
#' @return name of gene symbol
#'
getGeneSymbol <- function(thisKEGGSpecies) {
    switch(thisKEGGSpecies,
    mmu = "mgi_symbol",
    hsa = "hgnc_symbol",
    rno = "rgd_symbol")
}

#' Convert input species to KEGG species with flag
#'
#' @param inputSpecies human, mouse, rat
#' @return species of KEGG format with flag,
#' human:- Homo sapiens,
#' mouse:- Mus musculus,
#' rat:- Rattus norvegicus
#'
speciesKEGGFlagConvert<- function(inputSpecies){
#mouse:"- Mus musculus"
#human:"- Homo sapiens"
#rat:"- Rattus norvegicus"
switch(inputSpecies,
      mmu = "- Mus musculus",
      hsa = "- Homo sapiens",
      rno = "- Rattus norvegicus")
}

#' Mapping input file with ID to symbol, entrez, ensembl IDs
#'
#' @param filename input file in csv format
#' @param IDColumn must be numberic,the column number of sample ID
#' @param logFCColumn must be numberic,
#' the column number of sample log fold change
#' @param IDType Human: entrezgene, hgnc_symbol, ensembl_gene_id,
#' Mouse: entrezgene, mgi_symbol, ensembl_gene_id,
#' Rat: entrezgene, rgd_symbol, ensembl_gene_id
#' @param inputSpecies human, mouse, rat
#' @export
#' @return sample with entrez ID, symbol and ensembl ID
#' @examples
#' path<-system.file(package = "Key2Enrich")
#' filePath<-paste(path,"/extdata",sep="")
#' file<-paste(filePath,sep="","/sampleFile.csv")
#' \donttest{
#' thisSampleWith3IDs<-sampleWith3IDs(file,
#'                                    IDColumn=1,
#'                                    logFCColumn=2,
#'                                    IDType="mgi_symbol",
#'                                    inputSpecies="mouse")
#' }

    sampleWith3IDs<-function (filename,
                              IDColumn,logFCColumn,
                              IDType,inputSpecies){
    sample<-readInputFile(filename,IDColumn,logFCColumn,IDType)
    IDColValue<-sample[,(names(sample)==IDType)]
    IDMapping<-getAllTypesID(inputSpecies,IDType,IDColValue)
    inputSampleWith3IDs<-merge(sample,IDMapping,by.x=IDType,by.y=IDType)
    return (inputSampleWith3IDs)
    }