mergeIBDsegmentLists {hapFabia} | R Documentation

## 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

    ## 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]]))

[Package hapFabia version 1.29.0 Index]