R: Runs DNAcopy in parallel mode

dnaCopySf {cn.farms}

R Documentation

Runs DNAcopy in parallel mode

Description

This function even works very well with ff matrices,

Usage

dnaCopySf(x, chrom, maploc, cores = 1, smoothing, ...)

Arguments

`x`	A matrix with data of the copy number experiments
`chrom`	The chromosomes (or other group identifier) from which the markers came
`maploc`	The locations of marker on the genome
`cores`	Number of cores to use
`smoothing`	States if smoothing of the data should be done
`...`	Further parameter for the function segment of DNAcopy

Value

An instance of ExpressionSet containing the segments.

Author(s)

Djork-Arne Clevert okko@clevert.de and Andreas Mitterecker mitterecker@bioinf.jku.at

Examples

load(system.file("exampleData/mlData.RData", package = "cn.farms"))
mlData <- mlData[, 1:3]
colnames(assayData(mlData)$L_z) <- sampleNames(mlData)
segments <- dnaCopySf(
        x         = assayData(mlData)$L_z,
        chrom     = fData(mlData)$chrom,
        maploc    = fData(mlData)$start,
        cores     = 1,
        smoothing = FALSE)
fData(segments)

[Package cn.farms version 1.28.0 Index]