setStatistics: Computes and stores the statistics of an IBD segment list

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

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)

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