SeqGSEA (version 1.12.0)

topDEGenes: 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.

Value

A table for top n DE genes with significance metrics.

Details

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

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")