add_kegg_up_down_link: add links for the KEGG enrichment table.

In jmzeng1314/humanid: gene id annotation

Description

KEGG enrichment table comes from the stantard hyperG test. the PathwayID and pathway_name columns are needed. logFC <- DEG$logFC;names(logFC) <- DEG$symbol diff_gene_list also comes from DEG results.

Usage

add_kegg_up_down_link(keggEnrichTable, logFC, diff_gene_list, prefix = "test")

Arguments

keggEnrichTable	a data.frame which must have PathwayID and pathway_name columns
logFC	A numeric vector, the names for the vector are gene lists.
diff_gene_list	a vector which contain the significantly DEGs. symbol or entrez ID.
prefix	The prefix for all of the output files.

Value

write a html file with links for the keggEnrichTable

Examples

#' add_kegg_up_down_link(keggEnrichTable , DEG , diff_gene_list,prefix)

jmzeng1314/humanid documentation built on May 19, 2019, 2:57 p.m.