getDPIP: Compute differential patterns of isoform pairs from X2 test...

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

Compute differential patterns of isoform pairs from X2 test between group labels of cells and assignment of cells to components of the mixture models

Description

Compute differential patterns of isoform pairs from X2 test between group labels of cells and assignment of cells to components of the mixture models

Usage

getDPIP(cellCompMat.prob, group.label, usePermutation = TRUE,
  per.num = 10000, useParallel = TRUE)

Arguments

cellCompMat.prob	A results from assignCellComp function
group.label	A vector of group label of cells
usePermutation	An option to compute empirical p-values
per.num	The number of permutations when usePermutation=TRUE
useParallel	An option for using parallel (=TRUE)

Value

A list containing model-based theoretical p-values (t.VAL) and permutation-based empirical p-values (e.PVAL)

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)
#library(doParallel)
#registerDoParallel(cores=4)
set.seed(2015)
iso.pair.names=names(model.res$nq.list)
map.res=assignCellComp(iso.pair.names,model.res$dmix.list,
       model.res$nq.list, isoformLevel.data=isoformDataSample)
group.label=unlist(lapply(colnames(isoformDataSample),function(x) unlist(strsplit(x,"_"))[1]))
res=getDPIP(map.res$cellCompMat.prob,group.label,usePermutation=TRUE,per.num=100,useParallel=FALSE)
hist(res$e.PVAL, breaks=10)

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