nBreakpoints: Number of breakpoints

In sigaR: Statistics for Integrative Genomics Analyses in R

Description

The number of samples with at least one breakpoint is calculated for each transcipt.

Usage

nBreakpoints(featuresAndWeights, CNdata)

Arguments

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 subsetting of 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.
CNdata	Object of class cghCall

Details

For each item of the object featuresAndWeights the segmented data from the cghCall-object is used to determine whether a sample exhibits a breakpoint for this transcript.

Value

Object of class numeric containing the number of samples with at least one breakpoint. It is of the same length as the featuresAndWeights-object.

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", submitted for publication.

See Also

matchAnn2Ann.

Examples

# load data
data(pollackCN16)
data(pollackGE16)

# extract genomic information from cghCall-object
chr1 <- fData(pollackCN16)[,1]
bpstart1 <- fData(pollackCN16)[,2]
bpend1 <- fData(pollackCN16)[,3]

# extract genomic information from ExpressionSet-object
chr2 <- fData(pollackGE16)[,1]
bpstart2 <- fData(pollackGE16)[,2]
bpend2 <- fData(pollackGE16)[,3]

# match features from both platforms
matchedIDs <- matchAnn2Ann(chr1, bpstart1, bpend1, chr2, bpstart2, 
	bpend2, method = "distance", maxDist = 10000) 

# extract ids for object subsetting
matchedIDsCN <- lapply(matchedIDs, function(Z){ return(Z[, -1, drop=FALSE]) }) 

# calculate the number of breakpoints
nBreakpoints(matchedIDsCN, pollackCN16) 

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