doMixtureModelGene: Do mixture modelling for all pairs of isoforms of the same...

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

Do mixture modelling for all pairs of isoforms of the same single individual gene

Description

Do mixture modelling for all pairs of isoforms of the same single individual gene

Usage

doMixtureModelGene(isoMat, geneName = "geneName", usePlot = FALSE,
  useMixModel = TRUE, zero.thres = 0.05, nq.num = 3, tbreak = NULL,
  group.label = NULL)

Arguments

isoMat	Data matrix contains isoforms of a same individual gene. Each row indicates a isoform, while each column presents a cell
geneName	A string contains the name of gene that the isoforms are sharing
usePlot	A boolean value to allow plotting data and results. By default usePlot=FALSE
useMixModel	A boolean value to allow implementing the mixture model. By default useMixModel=TRUE
zero.thres	The threshold to separate components from null component p0. See doMixtureModelIsoformPair function
nq.num	The maximum components of the mixture model. See doMixtureModelIsoformPair function
tbreak	The number of breaks to create bins. See doMixtureModelIsoformPair function
group.label	The group label of cells used for pair plotting

Value

Lists of results of mixture models for isoform paires

Examples

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)))
isoMat=isoformDataSample[c(1,2),]
res=doMixtureModelGene(isoMat,geneName="118424",tbreak=tbreak)

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