mergeIBDsegmentLists: Merging IBD segments

In hapFabia: hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data

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

## S4 method for signature 'IBDsegmentList,ANY,vector'
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.

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.

Value

IBDsegmentListmerge

object of IBDsegmentList containing the merged IBD segments.

Author(s)

Sepp Hochreiter

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]]))

hapFabia documentation built on Nov. 8, 2020, 5:17 p.m.