topDEGenes {SeqGSEA} | R Documentation |
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.
topDEGenes(DEGres, n = 20, sortBy = c("padj", "pval", "perm.pval", "perm.padj", "NBstat", "foldChange"))
DEGres |
DE analysis results. |
n |
the number of top DE genes. |
sortBy |
indicating which method to rank genes. |
If the sortBy method is not among the column names, the function will result in an error.
A table for top n DE genes with significance metrics.
Xi Wang, xi.wang@newcastle.edu.au
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")