splitMatchingAtBreakpoints: Split matching at breakpoints

In sigaR: Statistics for Integrative Genomics Analyses in R

Description

In case a feature of platform 1 has been matched to multiple features of another platform, instead of averaging the data from these features, one may consider splitting the data at breakpoints within genes. This function modifies the results from the matching function matchAnn2Ann to facilitate this. The result can than directly be used in the subsetting functions cghCall2weightedSubset and ExpressionSet2weightedSubset.

Usage

splitMatchingAtBreakpoints(matchedIDs, CNdata)

Arguments

matchedIDs	An object of class list, as returned by the matchAnn2Ann-function.
CNdata	Object of class cghCall.

Value

An object of class list, similar to that returned by the matchAnn2Ann-function.

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, cghCall2weightedSubset, ExpressionSet2weightedSubset.

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
matchedFeatures <- matchAnn2Ann(chr1, bpstart1, bpend1, chr2, 
	bpstart2, bpend2, method = "distance", maxDist = 10000) 

# expand
matchedFeatures <- splitMatchingAtBreakpoints(matchedFeatures, pollackCN16) 

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