cghSeg2weightedSubset: Weighted subsetting cghSeg-objects.

In sigaR: Statistics for Integrative Genomics Analyses in R

Description

Limit an cghSeg object to a subset of its features, using weighted averaging of the copy number signal.

Usage

cghSeg2weightedSubset(CNdata, featuresAndWeights, chr, bpstart, 
bpend, ncpus = 1, verbose=TRUE)

Arguments

CNdata	Object of class cghSeg.
featuresAndWeights	Object of class list. Each list item is a matrix. The first column of this matrix contains the row numbers of features to be maintained in the cghSeg-object. The second column contains the weights of each features, to be used in the calculation of the weighted average copy number signal.
chr	Column in the slot featureData of the cghSeg-object specifying the chromosome information of the features.
bpstart	Column in the slot featureData of the cghSeg-object specifying the start basepair information of the features.
bpend	Column in the slot featureData of the cghSeg-object specifying the end basepair information of the features.
ncpus	Number of cpus to be used in computations.
verbose	Logical indicator: should intermediate output be printed on the screen?

Value

Object of class cghSeg, restricted to the specified subset of features.

Warning

The phenoData, experimentData, and other slots of the cghSeg-object are currently not passed on to the subsetted object.

Note

This is a more intricate version of the cghSeg2subset function. They exists parallel because this function is (much) slower than its counterpart.

Author(s)

Wessel N. van Wieringen: [e-mail]

References

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.

See Also

cghSeg2subset

Examples

# 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) 

sigaR documentation built on April 28, 2020, 6:05 p.m.