topGene: List top ranked DE genes

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

Description

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

Usage

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

Arguments

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

????????????????????

Details

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

Value

A data frame with following columns:

Author(s)

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

See Also

twoPhaseDE

Examples

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## 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)

zhijinwu/SC2P documentation built on May 16, 2019, 9:13 p.m.