doMixtureModelMatrix: Run mixture models for a data matrix of isoform expression

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

Run mixture models for a data matrix of isoform expression

Description

Run mixture models for a data matrix of isoform expression

Usage

doMixtureModelMatrix(isoformLevel.data, txdb = NULL, usePlot = FALSE,
  useMixModel = TRUE, zero.thres = 0.05, nq.num = 3, fn.out = NULL,
  tbreak = NULL, group.label = NULL)

Arguments

isoformLevel.data	A data matrix of isoform expression
txdb	A txdb of annotation reference
usePlot	A boolean value to allow plotting data and results, usePlot=FALSE (default)
useMixModel	A boolean value to allow implementing the mixture model, useMixModel=TRUE (default)
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
fn.out	File name of RData to export results
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 detected mixture models, AIC scores, number of components and state 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)))
res=doMixtureModelMatrix(isoformLevel.data=isoformDataSample,txdb=txdb,tbreak=tbreak)

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