KEGGenrich_blastkoala: KEGG pathway enrichment tools for blastkoala ko annotation.

In biomarble/PlantNGSTools: NGS bioinformatics tools for plants

KEGG pathway enrichment tools for blastkoala ko annotation.

Description

do KEGG pathway enrichment by a list of degs. Using blastkoala method to convert from GeneID to KEGG ID.

Usage

KEGGenrich_blastkoala(
  deglist,
  blastkoalafile,
  taxonid = "ko",
  outdir = NULL,
  outprefix,
  useFDR = FALSE
)

Arguments

deglist	DEG vector
blastkoalafile	blastkoala output file path, Gene ID to KEGG ID pair by row
taxonid	KEGG pathway taxon id prefix , for example, osa is for Oryza Sativa. available ids : https://www.genome.jp/kegg-bin/find_org_www?mode=abbr&obj=mode.map
outdir	output directory
outprefix	output file prefix
useFDR	whether to add FDR column

biomarble/PlantNGSTools documentation built on Feb. 8, 2024, 2:46 a.m.