topDEGenes {SeqGSEA}R Documentation

Extract top differentially expressed genes.

Description

This function is to extract top n differentially expressed genes, ranked by either DESeq p-values, DESeq adjusted p-values, permutation p-values, permutation adjusted p-values, or NB-statistics.

Usage

topDEGenes(DEGres, n = 20, 
           sortBy = c("padj", "pval", "perm.pval", "perm.padj", "NBstat", "foldChange"))

Arguments

DEGres

DE analysis results.

n

the number of top DE genes.

sortBy

indicating which method to rank genes.

Details

If the sortBy method is not among the column names, the function will result in an error.

Value

A table for top n DE genes with significance metrics.

Author(s)

Xi Wang, xi.wang@newcastle.edu.au

See Also

topDSGenes, topDSExons

Examples

data(RCS_example, package="SeqGSEA")
geneCounts <- getGeneCount(RCS_example)
label <- label(RCS_example)
DEG <- runDESeq(geneCounts, label)
permuteMat <- genpermuteMat(RCS_example, times=10)
DEGres <- DENBTest(DEG)
DEpermNBstat <- DENBStatPermut4GSEA(DEG, permuteMat)
DEGres <- DEpermutePval(DEGres, DEpermNBstat) 
topDEGenes(DEGres, n = 10, sortBy = "NBstat")

[Package SeqGSEA version 1.24.0 Index]