topDEGenes: Extract top differentially expressed genes.

In sunlightwang/SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

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, [e-mail]

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")

sunlightwang/SeqGSEA documentation built on Dec. 5, 2020, 5:52 p.m.