findDenseRegions
: R implementation of findDenseRegions
.
Extracts histogram bins which counts are larger than a threshold. Only values larger than a given quantile are considered.
findDenseRegions(obs,p=0.9,inte=500,thres=11,off=0)
obs
are included into the histogram.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.
S. Hochreiter et al., FABIA: Factor Analysis for Bicluster Acquisition, Bioinformatics 26(12):1520-1527, 2010.
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
data(res)
ib <- findDenseRegions(L(res)[,1],p=0.9,
inte=50,thres=6,off=0)
print(ib$len)
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