dnaCopySf {cn.farms} | R Documentation |
This function even works very well with ff matrices,
dnaCopySf(x, chrom, maploc, cores = 1, smoothing, ...)
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 |
An instance of ExpressionSet
containing the segments.
Djork-Arne Clevert okko@clevert.de and Andreas Mitterecker mitterecker@bioinf.jku.at
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)