mergeIBDsegmentLists {hapFabia} | R Documentation |
mergeIBDsegmentLists
: R implementation of mergeIBDsegmentLists
.
Merges and combines the IBD segments of one or two list(s).
A vector gives for each cluster in the
IBD segment list its new cluster membership as an integer
number.
Called by hapFabia
where new membership is determined by
hierarchical clustering.
## S4 method for signature 'IBDsegmentList,ANY,vector' mergeIBDsegmentLists(IBDsegmentList1,IBDsegmentList2=NULL,clustIBDsegmentList)
IBDsegmentList1 |
object of class |
IBDsegmentList2 |
optional: second object of class IBDsegmentList. |
clustIBDsegmentList |
vector giving for each cluster in the IBD segment list its new cluster membership as an integer number. |
A vector gives for each IBD segment its new membership as an integer number. IBD segments that belong to the same new cluster are merged.
Implementation in R.
IBDsegmentListmerge |
object of |
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) IBDsegmentList1 <- hapRes$IBDsegmentList1 IBDsegmentList2 <- hapRes$IBDsegmentList2 comp <- compareIBDsegmentLists(IBDsegmentList1, IBDsegmentList2,simv="minD",pTagSNVs=NULL, pIndivid=NULL,minTagSNVs=6,minIndivid=2) if (!is.null(comp)) { clustIBDsegmentList <- cutree(comp,h=0.8) mergedIBDsegmentList <- mergeIBDsegmentLists(IBDsegmentList1= IBDsegmentList1,IBDsegmentList2= IBDsegmentList2,clustIBDsegmentList= clustIBDsegmentList) } summary(IBDsegmentList1) summary(IBDsegmentList2) summary(mergedIBDsegmentList) print(IBDsegmentPos(mergedIBDsegmentList[[1]])) print(IBDsegmentLength(mergedIBDsegmentList[[1]]))