topGene: List top ranked DE genes
In zhijinwu/SC2P: Two phase differential expression for singel-cell RNA-seq

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

Given DE test results, provide a list of top ranked DE genes according to user specified criteria

1	topGene(de.obj, phase = "both", number = 20, p.value = 0.05, adjust.method = "BH", annotation = NULL)

`de.obj`	A data frame for DE test result, must be returned from twoPhaseDE.
`phase`	Character to indicate the phase for DE gene to be listed. Available options include '1' for phase I; '2' for phase II; and "both" for both phases.
`number`	Integer for number of genes to be listed.
`p.value`	????????????
`adjust.method`	??????????????????
`annotation`	????????????????????

HOW TO RANK GENES WHEN 'BOTH' IS THE OPTION????

A data frame with following columns:

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)

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

## report top ranked genes in phase I
topGene(de.sc2p, 1)

## report top ranked genes in phase II
topGene(de.sc2p, 2)

## report top ranked genes in both phases
topGene(de.sc2p, phase="both", number=5)


## End(Not run)