eset2Phase: Estimate the phases of expression
In zhijinwu/SC2P: Two phase differential expression for singel-cell RNA-seq

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

This function estimates the probabilities of expression for all genes in all cells. Given an ExpressionSet, it returns the posterior probability for being in phase II (expression) for each gene in each cell.

1	eset2Phase(eset, low.prob = 0.99)

`eset`	An object of ExpressionSet for the single cell RNA-seq data. This should be constructed using the ExpressionSet function provided by Biobase.
`low.prob`	The probability threshold for calling phase II. When the posterior probability for a gene in a cell is greater than this threshold, it will be called as in phase II (expressed).

The estimation procedure considers the cell-specific (for example, sequencing depth and marginal distribution of expression for all genes), and gene-specific (for example, average expression level for this gene cross all cells) factors, which achieves a data-driven thresholding and provides better results than using an fixed, ad hoc threshold for determining expression state.

An object of sc2pSet, which is an extension of ExpressionSet.

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

twoPhaseDE

## 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

## visualize the results for a gene
zyPlot(rownames(data)[1], data, group.name="celltype")

## End(Not run)