detectSide: Detect sides of models

In nghiavtr/ISOP: Isoform-Level Expression Patterns in Single-cell RNA-sequencing Data

Detect sides of models

Description

Detect sides of models

Usage

detectSide(dmix.list, nq.vec)

Arguments

dmix.list	A list of detected models
nq.vec	A vector of number of components of detected models

Value

A vector consisting of sides of models

Examples

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))

nghiavtr/ISOP documentation built on April 21, 2023, 3:57 p.m.