cghSeg2weightedSubset {sigaR} | R Documentation |
Limit an cghSeg
object to a subset of its features, using weighted averaging of the copy number signal.
cghSeg2weightedSubset(CNdata, featuresAndWeights, chr, bpstart, bpend, ncpus = 1, verbose=TRUE)
CNdata |
Object of class |
featuresAndWeights |
Object of class |
chr |
Column in the slot |
bpstart |
Column in the slot |
bpend |
Column in the slot |
ncpus |
Number of cpus to be used in computations. |
verbose |
Logical indicator: should intermediate output be printed on the screen? |
Object of class cghSeg
, restricted to the specified subset of features.
The phenoData
, experimentData
, and other slots of the cghSeg
-object are currently not passed on to the subsetted object.
This is a more intricate version of the cghSeg2subset
function. They exists parallel because this function is (much) slower than its counterpart.
Wessel N. van Wieringen: w.vanwieringen@vumc.nl
Van Wieringen, W.N., Unger, K., Leday, G.G.R., Krijgsman, O., De Menezes, R.X., Ylstra, B., Van de Wiel, M.A. (2012), "Matching of array CGH and gene expression microarray features for the purpose of integrative analysis", BMC Bioinformatics, 13:80.
cghSeg2subset
# load data data(pollackCN16) # extract genomic information from ExpressionSet-object chr <- fData(pollackCN16)[,1] bpstart <- fData(pollackCN16)[,2] bpend <- fData(pollackCN16)[,3] # find unique genomic locations uniqInfo <- uniqGenomicInfo(chr, bpstart, bpend, verbose = FALSE) # transform the cghCall-object to a cghSeg-object pollackCN16 <- cghCall2cghSeg(pollackCN16) # subset cghSeg-object to features with unique genomic locations pollackCN16 <- cghSeg2weightedSubset(pollackCN16, uniqInfo, 1, 2, 3)