dnaCopySf: Runs DNAcopy in parallel mode

In cn.farms: cn.FARMS - factor analysis for copy number estimation

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 [e-mail] and Andreas Mitterecker [e-mail]

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)

cn.farms documentation built on Nov. 8, 2020, 7:59 p.m.