extractSignatures: Extract Signatures

In dami82/mutSignatures_dev: Decipher Mutational Signatures from Somatic Mutational Catalogs

Usage

extractSignatures(mutCountMatrix, params, bootStrap = TRUE)

Arguments

mutCountMatrix
params
bootStrap

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 (mutCountMatrix, params, bootStrap = TRUE) 
{
    num_processesToExtract <- params$num_processesToExtract
    approach <- params$approach
    algorithm <- params$algorithm
    eps <- params$eps
    if (bootStrap) {
        bstrpd.result <- bootstrapCancerGenomes(mutCountMatrix)
    }
    else {
        bstrpd.result <- mutCountMatrix
    }
    bstrpd.result[bstrpd.result < eps] <- eps
    if (algorithm %in% c("brunet", "alexa")) {
        nmf.results <- alexaNMF(v = bstrpd.result, r = num_processesToExtract, 
            params = params)
    }
    else {
        nmf.results <- chihJenNMF(v = bstrpd.result, r = num_processesToExtract, 
            params = params)
    }
    tmp.w <- nmf.results$w
    tmp.h <- nmf.results$h
    for (jj in 1:num_processesToExtract) {
        tmp.tot <- sum(tmp.w[, jj])
        tmp.w[, jj] <- tmp.w[, jj]/tmp.tot
        tmp.h[jj, ] <- tmp.h[jj, ] * tmp.tot
    }
    mutCountMatrix.reconstructed <- tmp.w %*% tmp.h
    result.list <- list()
    result.list$Wk <- tmp.w
    result.list$Hk <- tmp.h
    result.list$mutCounts.reconstructed <- mutCountMatrix.reconstructed
    result.list$mutCounts.errors <- bstrpd.result - mutCountMatrix.reconstructed
    if (params$logIterations != "lite") {
        result.list$inputMatrix <- bstrpd.result
        result.list$cosDist <- proxy::dist(rbind(as.vector(bstrpd.result), 
            as.vector(mutCountMatrix.reconstructed)), method = "cosine")[1]
    }
    return(result.list)
  }

dami82/mutSignatures_dev documentation built on May 17, 2019, 7:02 p.m.