findDenseRegions: Find accumulations of values via histogram counts

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

Description

findDenseRegions: R implementation of findDenseRegions.

Extracts histogram bins which counts are larger than a threshold. Only values larger than a given quantile are considered.

Usage

findDenseRegions(obs,p=0.9,inte=500,thres=11,off=0)

Arguments

obs	values for constructing the histogram.
p	quantile above which the values of obs are included into the histogram.
inte	size of the histogram bins.
thres	threshold for histogram counts: bin with counts larger equal the threshold are selected.
off	offset of the histogram bin positions.

Details

Extracts histogram bins which counts are larger than a threshold. The threshold is supplied and can be computed according to some assumptions on expected bin counts. Only values larger than a given quantile are considered.

Implementation in R.

Value

list with

m	vector of locations of the selected bin (middle of bins).
l	vector of lengths of the bins.
pos	list where each element is a vector of locations of values that contributed to the counts (SNV positions).
len	vector of counts or equivalently vector of the number of SNVs.

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(res)
ib <- findDenseRegions(L(res)[,1],p=0.9,
   inte=50,thres=6,off=0)
print(ib$len)

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