hapFabia (version 1.14.0)

setStatistics: 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

"setStatistics"(IBDsegmentList)

Arguments

IBDsegmentList

object of class IBDsegmentList.

Value

object of class IBDsegmentList with statistics set

Details

The list can be extended by the user.

Implementation in R.

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)