doMixtureModelIsoformPair: Do mixture modelling for two isoforms

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

Do mixture modelling for two isoforms

Description

Do mixture modelling for two isoforms

Usage

doMixtureModelIsoformPair(x0, x1, nq.num = 3, tbreak = NULL,
  zero.thres = 0.05, min.prop = 0.025)

Arguments

x0	A vector of data points from isoform 1
x1	A vector of data points from isoform 2
nq.num	The maximum components of the mixture model
tbreak	The number of breaks to create bins
zero.thres	The threshold to separate components from null component p0
min.prop	Minimum proportion threshold for a component in the mixture model

Value

A list consisting of list of mixture models (dmix.list), index of the best model (AIC.min.Id), vector of AIC scores (AIC.score), ...

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)))
x0=isoformDataSample[1,]
x1=isoformDataSample[2,]
res=doMixtureModelIsoformPair(x0,x1,tbreak=tbreak)

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