cghCall2maximumSubset {sigaR} | R Documentation |
Limit an cghCall
object to a subset of its features, selecting those features with the most deviating copy number signal.
cghCall2maximumSubset(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? |
Per entry of the featuresAndWeights
-object and per sample the feature with the maximum absolute segmented DNA copy number signal is selected.
Object of class cghCall
, restricted to the specified subset of features.
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.
# 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) # subset cghCall-object to features with unique genomic locations pollackCN16 <- cghCall2maximumSubset(pollackCN16, uniqInfo, 1, 2, 3)