addWeak: Add Weak Mutation Types

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

Usage

addWeak(mutationTypesToAddSet, processes_I, processesStd_I, Wall_I, genomeErrors_I, genomesReconstructed_I)

Arguments

mutationTypesToAddSet
processes_I
processesStd_I
Wall_I
genomeErrors_I
genomesReconstructed_I

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 (mutationTypesToAddSet, processes_I, processesStd_I, 
    Wall_I, genomeErrors_I, genomesReconstructed_I) 
{
    if (length(mutationTypesToAddSet) > 0 & mutationTypesToAddSet[1] > 
        0) {
        totalMutTypes <- nrow(Wall_I) + length(mutationTypesToAddSet)
        processes <- matrix(0, nrow = totalMutTypes, ncol = ncol(processes_I))
        processesStd <- matrix(0, nrow = totalMutTypes, ncol = ncol(processesStd_I))
        Wall <- matrix(0, nrow = totalMutTypes, ncol = ncol(Wall_I))
        genomeErrors <- lapply(1:length(genomeErrors_I), (function(i) {
            matrix(0, nrow = totalMutTypes, ncol = ncol(genomeErrors_I[[1]]))
        }))
        genomesReconstructed <- lapply(1:length(genomesReconstructed_I), 
            (function(i) {
                matrix(0, nrow = totalMutTypes, ncol = ncol(genomesReconstructed_I[[1]]))
            }))
        origArrayIndex <- 1
        for (i in 1:totalMutTypes) {
            if (!(i %in% mutationTypesToAddSet)) {
                processes[i, ] <- processes_I[origArrayIndex, 
                  ]
                processesStd[i, ] <- processesStd_I[origArrayIndex, 
                  ]
                Wall[i, ] <- Wall_I[origArrayIndex, ]
                for (j in 1:length(genomeErrors_I)) {
                  genomeErrors[[j]][i, ] <- genomeErrors_I[[j]][origArrayIndex, 
                    ]
                }
                for (j in 1:length(genomesReconstructed_I)) {
                  genomesReconstructed[[j]][i, ] <- genomesReconstructed_I[[j]][origArrayIndex, 
                    ]
                }
                origArrayIndex <- origArrayIndex + 1
            }
        }
    }
    else {
        processes <- processes_I
        processesStd <- processesStd_I
        Wall <- Wall_I
        genomeErrors <- genomeErrors_I
        genomesReconstructed <- genomesReconstructed_I
    }
    weakAdded.list <- list()
    weakAdded.list$processes <- processes
    weakAdded.list$processesStd <- processesStd
    weakAdded.list$Wall <- Wall
    weakAdded.list$mutCountErrors <- genomeErrors
    weakAdded.list$mutCountReconstructed <- genomesReconstructed
    return(weakAdded.list)
  }

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