hapFabia (version 1.14.0)

mergeIBDsegmentLists: Merging IBD segments

Description

mergeIBDsegmentLists: R implementation of mergeIBDsegmentLists.

Merges and combines the IBD segments of one or two list(s). A vector gives for each cluster in the IBD segment list its new cluster membership as an integer number. Called by hapFabia where new membership is determined by hierarchical clustering.

Usage

"mergeIBDsegmentLists"(IBDsegmentList1,IBDsegmentList2=NULL,clustIBDsegmentList)

Arguments

IBDsegmentList1

object of class IBDsegmentList.

IBDsegmentList2

optional: second object of class IBDsegmentList.

clustIBDsegmentList

vector giving for each cluster in the IBD segment list its new cluster membership as an integer number.

Value

IBDsegmentListmerge

object of IBDsegmentList containing the merged IBD segments.

Details

A vector gives for each IBD segment its new membership as an integer number. IBD segments that belong to the same new cluster are merged.

Implementation in R.

References

S. Hochreiter et al., ‘FABIA: Factor Analysis for Bicluster Acquisition’, Bioinformatics 26(12):1520-1527, 2010.

See Also

IBDsegment-class, IBDsegmentList-class, analyzeIBDsegments, compareIBDsegmentLists, extractIBDsegments, findDenseRegions, hapFabia, hapFabiaVersion, hapRes, chr1ASW1000G, IBDsegmentList2excel, identifyDuplicates, iterateIntervals, makePipelineFile, matrixPlot, mergeIBDsegmentLists, mergedIBDsegmentList, plotIBDsegment, res, setAnnotation, setStatistics, sim, simu, simulateIBDsegmentsFabia, simulateIBDsegments, split_sparse_matrix, toolsFactorizationClass, vcftoFABIA

Examples

data(hapRes)
IBDsegmentList1 <- hapRes$IBDsegmentList1
IBDsegmentList2 <- hapRes$IBDsegmentList2
comp <-
compareIBDsegmentLists(IBDsegmentList1,
   IBDsegmentList2,simv="minD",pTagSNVs=NULL,
   pIndivid=NULL,minTagSNVs=6,minIndivid=2)
if (!is.null(comp)) {
  clustIBDsegmentList <- cutree(comp,h=0.8)
  mergedIBDsegmentList <-
     mergeIBDsegmentLists(IBDsegmentList1=
     IBDsegmentList1,IBDsegmentList2=
     IBDsegmentList2,clustIBDsegmentList=
     clustIBDsegmentList)
}
summary(IBDsegmentList1)
summary(IBDsegmentList2)

summary(mergedIBDsegmentList)
print(IBDsegmentPos(mergedIBDsegmentList[[1]]))
print(IBDsegmentLength(mergedIBDsegmentList[[1]]))