twoPhaseDE: Two-phase differential expression test for scRNA-seq data
In zhijinwu/SC2P: Two phase differential expression for singel-cell RNA-seq

Description Usage Arguments Details Value Author(s) See Also Examples

This function performs differential expression analysis for singel-cell RNA-seq data in two phases: phase transition (probability of being expressed), and magnitude tuning (levels of expression once the gene is on). Currently the function only works for the comparison of two biological conditions.

1	twoPhaseDE(sc2p.obj, design, test.which, low.prob = 0.99, offset = c("SC2P", "sf"))

`sc2p.obj`	An object of sc2pSet. Should be the result object from 'eset2Phase' function.
`design`	A character vector of variable names in pData(sc2p.obj) to provide regression covariates in DE test.
`test.which`	An integer for the index of the to-be-tested binary variable in argument 'design'.
`low.prob`	xxxxxxxxxxxxxx What's this???
`offset`	Indicates the method to compute normalization factor. 'SC2P' is the normalization procedure provided by SC2P. 'sf' uses the total counts in cells as normalizing constant.

est2Phase needs to be called before this function to estimate the probabilities of being in two states.

A data frame with following columns:

`p1`
`p2`
`Ph1.coef`
`Ph1.pval`
`m1`
`m2`
`Ph2.coef`
`Ph2.ci.lo`
`Ph2.ci.hi`
`Ph2.pval`
`logFC`	Log fold change

The data frame is sorted by gene names alphabetically.

Zhijin (Jean) Wu <zwu@stat.brown.edu>

est2Phase, topGene, visGene

## Not run: 
data(brain_scRNAseq)

## create ExpressionSet
colnames(Y) <- rownames(design)
phenoData <- new("AnnotatedDataFrame", data=design)
eset <- ExpressionSet(assayData=Y, phenoData=phenoData)

## estimate phases
data <- eset2Phase(eset)
data

##  DE test
de.sc2p <- twoPhaseDE(data, design="celltype", test.which=1, offset="sf")

## list top ranked DE genes
topGene(de.sc2p, phase=1)
topGene(de.sc2p, phase=2)
topGene(de.sc2p, phase="both")

## visualize top DE gene in phase 2
visGene(topGene(de.sc2p, 2)$Gene.name[1], data, group.name="celltype")

## End(Not run)