setStatistics {hapFabia} | R Documentation |
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
:
"avIBDsegmentPosS": physical position
"avIBDsegmentLengthSNVS": length in SNVs
"avIBDsegmentLengthS": length in bp
"avnoIndividS": number individuals
"avnoTagSNVsS": number tagSNVs
"avnoFreqS": tagSNV frequency
"avnoGroupFreqS": tagSNV group frequency
"avnotagSNVChangeS": tagSNV change between minor and major allele
"avnotagSNVsPerIndividualS": tagSNVs per individual
"avnoindividualPerTagSNVS": individuals per tagSNV.
## S4 method for signature 'IBDsegmentList' setStatistics(IBDsegmentList)
IBDsegmentList |
object of class |
The list can be extended by the user.
Implementation in R.
object of class IBDsegmentList
with statistics set
Sepp Hochreiter
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(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)