setStatistics {hapFabia} | R Documentation

## Computes and stores the statistics of an IBD segment list

### Description

`setStatistics`: R implementation of `setStatistics`.

Computes the statistics of an IBD segment list given as an object of the class `IBDsegmentList`. In the slot `statistics` of an object of the class `IBDsegmentList` the summary statistics across the list of IBD segments are stored. Following characteristics are stored in the list `statistics`:

1. "avIBDsegmentPosS": physical position

2. "avIBDsegmentLengthSNVS": length in SNVs

3. "avIBDsegmentLengthS": length in bp

4. "avnoIndividS": number individuals

5. "avnoTagSNVsS": number tagSNVs

6. "avnoFreqS": tagSNV frequency

7. "avnoGroupFreqS": tagSNV group frequency

8. "avnotagSNVChangeS": tagSNV change between minor and major allele

9. "avnotagSNVsPerIndividualS": tagSNVs per individual

10. "avnoindividualPerTagSNVS": individuals per tagSNV.

### Usage

    ## S4 method for signature 'IBDsegmentList'
    setStatistics(IBDsegmentList)

### Arguments

`IBDsegmentList` | object of class `IBDsegmentList`.

### Details

The list can be extended by the user.

Implementation in R.

### Value

object of class `IBDsegmentList` with statistics set

### 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(hapRes)
    res <- hapRes$res
    sPF <- hapRes$sPF
    annot <- hapRes$annot
    nnL <- length(Z(res)[1,])
    labelsA <- cbind(as.character(1:nnL),as.character(1:nnL),
       as.character(1:nnL),as.character(1:nnL))
    resIBDsegmentList <-
      extractIBDsegments(res=res,sPF=sPF,annot=annot,
      chrom="1",labelsA=labelsA,ps=0.9,psZ=0.8,inteA=50,
      thresA=6,mintagSNVs=6,off=0,procMinIndivids=0.1,
      thresPrune=1e-3)

    summary(resIBDsegmentList)

    resIBDsegmentList <- setStatistics(resIBDsegmentList)

    summary(resIBDsegmentList)

[Package hapFabia version 1.28.0 Index]