dichotomize: Dichotomize Tumor data based on Methylation values of Normal...

In mbootwalla/MethylHose: Automated down stream processing of methylation data

Description

This function filters and dichotomizes Methylation values of Tumor samples based on the methylation values of Normal samples. This method accounts for the contamination of Tumor tissue with surrounding Normal tissue which routinely confounds methylation analysis of cancer samples

Usage

dichotomize(Mset, T, N, index.T, index.N, filter = c("none", "noncg", "sex", "snp", "rpt", "all", "custom"), custom.filter)

Arguments

Mset
T
N
index.T
index.N
filter
custom.filter

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (Mset, T, N, index.T, index.N, filter = c("none", "noncg", 
    "sex", "snp", "rpt", "all", "custom"), custom.filter) 
{
    if (!missing(Mset) && is(Mset, "MethylumiSet")) {
        if (!missing(T) && !missing(N)) 
            warning("Both MethyLumiSet and Tumor-Normal beta value matrices are provided. Using methyLumiSet for processing \n")
        if (missing(index.T) || missing(index.N)) 
            stop("Tumor and Normal sample indices are missing. Cannot process MethyLumiSet \n")
        beta <- betas(Mset)
    }
    if (missing(Mset) && (!missing(T) && (!missing(N)))) {
        if (!is(T, "matrix") && !is(N, "matrix")) 
            stop("Expect Tumor-Normal beta values to be matrices. Please provide valid matrices to proceed \n")
        beta <- cbind(T, N)
        if (missing(index.T) || missing(index.N)) {
            index.T <- 1:ncol(T)
            index.N <- (ncol(T) + 1):ncol(beta)
        }
    }
    if (!any(grepl("^cg", rownames(beta)))) 
        stop("Probe names are not standard Illumina 450k probe names \n")
    if (missing(filter)) {
        filter <- "all"
    }
    else {
        filter <- match.arg(filter, several.ok = TRUE)
    }
    if (!(all(filter %in% c("none", "noncg", "sex", "snp", "rpt", 
        "all", "custom")))) 
        stop("Please provide a valid filter. See '?applyFilters' for valid filters \n")
    beta.filtered <- applyFilters(beta, filter, custom.filter = custom.filter)
    beta.filtered <- na.omit(beta.filtered)
    gc()
    betaT.raw <- beta.filtered[, index.T, drop = FALSE]
    betaN.raw <- beta.filtered[, index.N, drop = FALSE]
    medianN <- apply(betaN.raw, 1, median, na.rm = T)
    probesN <- names(subset(medianN, medianN < 0.2))
    betaT.dichotomized <- betaT.raw[probesN, , drop = FALSE]
    betaT.dichotomized <- betaT.dichotomized > 0.3
    storage.mode(betaT.dichotomized) <- "numeric"
    betaN.dichotomized <- betaN.raw > 0.3
    storage.mode(betaN.dichotomized) <- "numeric"
    retval <- SimpleList()
    retval$RAW <- SimpleList(Tumor.Raw = betaT.raw, Normal.Raw = betaN.raw)
    retval$DICHOTOMIZED <- SimpleList(Tumor.Dichotomized = betaT.dichotomized, 
        Normal.Dichotomized = betaN.dichotomized)
    gc()
    return(retval)
  }

mbootwalla/MethylHose documentation built on May 22, 2019, 12:57 p.m.