nBreakpoints {sigaR} | R Documentation |
The number of samples with at least one breakpoint is calculated for each transcipt.
nBreakpoints(featuresAndWeights, CNdata)
featuresAndWeights |
Object of class |
CNdata |
Object of class |
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.
Object of class numeric
containing the number of samples with at least one breakpoint. It is of the same length as the featuresAndWeights
-object.
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", submitted for publication.
# 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)