R/GWAPMap.R

In MPIIComputationalEpigenetics/MAGAR: MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

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# GWAPMap.R
# created: 2020-07-30
# creator: Michael Scherer
# ---------------------------------------------------------------------------------------
# methods to import GWAS map output and for working with the results
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#'parseGWASMapOutput
#'
#'This method takes as input a path to a CSV file containing the GWASMap output
#'
#'@param    file The path to the GWASMap CSV file
#'@param    sep The table separator
#'@param    dec The decimal point separator
#'@return    A list object with each element being the first line of the GWASMap output file.
#'        Each of the distinct elements in the first column is used as a category and the associated
#'        table is parsed separately as a table.
#'@noRd
#'@author    Michael Scherer
parseGWASMapOutput <- function(file,
                sep=",",
                dec="."){
    first.line <- unlist(read.table(file,sep=sep,nrows=1))
    first.line[is.na(first.line)] <- ""
    has.info <- sapply(first.line,nchar)
    parts <- sum(has.info>0)
    res <- list()
    i <- 1
    done <- rep(FALSE,length(first.line))
    while(!all(done)){
        done[seq(1,i)] <- TRUE
        n <- (min(c(which(has.info>0&!done),length(first.line)))-1)
        cols.to.read <- rep("NULL",length(first.line))
        cols.to.read[i:n] <- NA
        dat.table <- read.table(file,
                sep=sep,
                header=TRUE,
                skip=1,
                colClasses=cols.to.read,
                dec=dec)
        res[[first.line[i]]] <- dat.table
        i <- (n+1)
    }
    return(res)
}