R/getSNPlocations.R

In fischuu/GenomicTools: Collection of Tools for Genomic Data Analysis

getSNPlocations <- function(genotInfo, annot, th){
    if(!is.null(th)) if(th==0) th <- NULL
    if(!is.null(th)){
    # Go here, when the map is stored as data table
      if(is.data.table(genotInfo)){
        colnames(annot) <- c("Chr","Start","End")
        th <- th * 10^6
        chrSNPs <- genotInfo[genotInfo$V1==as.character(annot[1,1]),]
        lowSNPs <- chrSNPs[chrSNPs$V4>(annot$Start-th),]
        SNPs <- lowSNPs[lowSNPs$V4<(annot$End+th),]
        #    if(is.null(th)) SNPs <- chrSNPs
        output <- list(SNPloc=as.data.frame(SNPs),SNPcol=as.numeric(rownames(SNPs)))       
        
     # Take this, when the map is not yet stored as data table 
      } else {
        colnames(annot) <- c("Chr","Start","End")
        th <- th * 10^6
        genotInfo[,1] <- as.character(genotInfo[,1])
        chrSNPs <- genotInfo[genotInfo[,1]==as.character(annot[1,1]),]
        chrSNPs[,2] <- as.character(chrSNPs[,2])
        chrSNPs[,4] <- as.numeric(as.character(chrSNPs[,4]))  
        lowSNPs <- chrSNPs[chrSNPs[,4]>(annot$Start-th),]
        SNPs <- lowSNPs[lowSNPs[,4]<(annot$End+th),]
        #    if(is.null(th)) SNPs <- chrSNPs
        output <- list(SNPloc=SNPs,SNPcol=as.numeric(rownames(SNPs)))
      }
    } else {
      output <- list(SNPloc=genotInfo, SNPcol=rownames(genotInfo))
    }
  output
}