R/types.R

In oirot/tumorHeatmap: Visual comparison of mutational processes in a set of tumors

#' A list of the allowed signatures type
#'
#' This list contains all the allowed signature types.
#' Use alexandrov2 for Alexandrov V2 signatures,
#' alandrov32 for Alexandrov V3.2 ones and shiraishi for Shiraishi signatures.
#'
#' @examples
#' signatureTypes
#' signatureTypes$shiraishi
#' @export
signatureTypes <- list(
    alexandrov2="Alexandrov.2",
    alexandrov32="Alexandrov.32",
    shiraishi="Shiraishi"
)


.getGenomeType <- function(signatureType) {
    return(strsplit(signatureType, ".", fixed=TRUE)[[1]][1])
}


#' @importFrom utils read.table
.readAlexandrovV32Signatures <- function(filenames) {
    signatures <-
        as.matrix(read.table(
            filenames,
            sep="\t",
            header=TRUE,
            row.names=1
        ))
    ## get the names of the mutations and add them as names for the list
    ## splitting each column into diffrent list elements that represent a signature
    mutationIDs <- rownames(signatures)
    signatures <- split(signatures, col(signatures, as.factor = TRUE))
    signatures <- lapply(signatures, function(l) {
        names(l) <- mutationIDs
        return(l)
    })
    return(signatures)
}


#' @importFrom decompTumor2Sig readAlexandrovSignatures
#' @importFrom decompTumor2Sig readShiraishiSignatures
## vector of functions to read the allowd signature types
readSignaturesFunctions <-
    c(
        decompTumor2Sig::readAlexandrovSignatures,
        .readAlexandrovV32Signatures,
        decompTumor2Sig::readShiraishiSignatures
    )


## returns the correct function to read the signatures from the type
.getReadSignatureFunction <- function(type) {
    type <- match(type, signatureTypes)
    return(readSignaturesFunctions[[type]])
}