findDenseRegions {hapFabia} | R Documentation

## Find accumulations of values via histogram counts

### 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)

[Package hapFabia version 1.28.0 Index]