cghCall2maximumSubset: Maximum subsetting cghCall-objects.

In sigaR: Statistics for Integrative Genomics Analyses in R

Description

Limit an cghCall object to a subset of its features, selecting those features with the most deviating copy number signal.

Usage

cghCall2maximumSubset(CNdata, featuresAndWeights, chr, bpstart, 
bpend, ncpus = 1, verbose=TRUE)

Arguments

CNdata	Object of class cghCall.
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 cghCall-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 cghCall-object specifying the chromosome information of the features.
bpstart	Column in the slot featureData of the cghCall-object specifying the start basepair information of the features.
bpend	Column in the slot featureData of the cghCall-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?

Details

Per entry of the featuresAndWeights-object and per sample the feature with the maximum absolute segmented DNA copy number signal is selected.

Value

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

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

matchAnn2Ann

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) 

# subset cghCall-object to features with unique genomic locations
pollackCN16 <- cghCall2maximumSubset(pollackCN16, uniqInfo, 1, 2, 3) 

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