hapFabia (version 1.14.0)

compareIBDsegmentLists: Hierarchical clustering of IBD segments stored in IBD segment list(s)

Description

compareIBDsegmentLists: R implementation of compareIBDsegmentLists.

The IBD segments in one or two list(s) are compared by hierarchical clustering. Different similarity measures are available. Called by hapFabia.

Usage

"compareIBDsegmentLists"(IBDsegmentList1,IBDsegmentList2=NULL,simv="minD",pTagSNVs=NULL,pIndivid=NULL,minTagSNVs=6,minIndivid=2)

Arguments

IBDsegmentList1

list of IBD segments given as IBDsegmentList object.

IBDsegmentList2

optional: second list of IBD segments given as IBDsegmentList object.

simv

similarity measure: minD (percentage of the smaller set explained by the larger set), jaccard (Jaccard index), dice (Dice index), or maxD (percentage of the larger set explained by the smaller set); default minD.

pTagSNVs

optional: exponent for tagSNV similarity.

pIndivid

optional: exponent for individuals similarity.

minTagSNVs

required minimal number of overlapping SNVs to assign similarity different from zero; default 6.

minIndivid

required minimal number of overlapping individuals to assign similarity different from zero; default 2.

Value

clust

object of class hclust which describes the tree produced by the hierarchical clustering method.

Details

Similarities are separately computed for SNVs and for individuals using one of the similarity measure: "minD" (percentage of the smaller set explained by the larger set), "jaccard" (Jaccard index), "dice" (Dice index), or "maxD" (percentage of the larger set explained by the smaller set). One minus the product between SNV similarity and individuals similarity is the final value used for clustering.

The final similarity measure is not a distance but is symmetric, one for similarity of an IBD segment with itself, zero if either CNVs or individuals have no overlap, and between zero and one. Called by hapFabia.

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)

show(comp)