sim: Similarity measures for IBD segments

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

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)

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