sim {hapFabia} | R Documentation

## Similarity measures for IBD segments

### Description

`sim`: R implementation of `sim`.

Similarity measure for IBD segments, tagSNVs, and individuals.

### Usage

    sim(x,y,simv="minD",minInter=2)

### Arguments

`x` | first vector.
`y` | second vector.
`simv` | similarity measure: `"minD"` (percentage of smaller explained by larger set), `"jaccard"` (Jaccard index), `"dice"` (Dice index), or `"maxD"`; default `"minD"`.
`minInter` | minimal size of intersection that is required for a non-zero measure; default 2.

### Details

Similarity measure for IBD segments, tagSNVs, and individuals.

Implementation in R.

### Value

`erg` | the similarity measure between 0 and 1, where 0 is not similar and 1 is identical.

### 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

    x <- sample(1:15,8)
    y <- sample(1:15,8)
    sim(x,y,simv="minD",minInter=1)

[Package hapFabia version 1.28.0 Index]