detectSide | R Documentation |
Detect sides of models
detectSide(dmix.list, nq.vec)
dmix.list |
A list of detected models |
nq.vec |
A vector of number of components of detected models |
A vector consisting of sides of models
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
library("AnnotationDbi")
txdb=TxDb.Hsapiens.UCSC.hg19.knownGene
#The txdb also can be imported from a gtf file by using package GenomicFeatures
data(isoformDataSample)
#preprocessing
isoformDataSample=ifelse(isoformDataSample <= 3,0,isoformDataSample)
isoformDataSample=isoformDataSample[which(rowSums(isoformDataSample)>0),]
#tranform read count dataset to log scale
isoformDataSample=ifelse(isoformDataSample==0,0,log2(isoformDataSample))
#now data is ready
tbreak=round(sqrt(ncol(isoformDataSample)))
model.res=doMixtureModelMatrix(isoformLevel.data=isoformDataSample,txdb=txdb,tbreak=tbreak)
res=detectSide(dmix.list=model.res$dmix.list,nq.vec=unlist(model.res$nq.list))
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