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]