cn.farms (version 1.20.0)

dnaCopySf: 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.

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)