compareIBDsegmentLists {hapFabia} | R Documentation

## 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

    ## S4 method for signature
    ## 'IBDsegmentList,ANY,character,ANY,ANY,numeric,numeric'
    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.

### 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.

### Value

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

### 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)

    show(comp)

[Package hapFabia version 1.29.0 Index]