expandMatching2singleIDs {sigaR} | R Documentation |
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 maintaining all features, each matched individually the feature of platform 1.
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
.
expandMatching2singleIDs(matchedIDs)
matchedIDs |
An object of class |
An object of class list
, similar to that returned by the matchAnn2Ann
-function.
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", BMC Bioinformatics, 13:80.
matchAnn2Ann
, cghCall2weightedSubset
, ExpressionSet2weightedSubset
.
# 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 <- expandMatching2singleIDs(matchedFeatures)