I am having trouble grabbing specific pathway info using databases in R. I have RNAseq results and I want to remove immune related genes from the current list that I have.
With a vector of gene names/symbols from RNAseq , I queried org.hs.eg.db to grab entrezIDs keys etc.
I thought about trying to use pathids from this database which I think are KEGG pathway ids which I can subsequently filter out the appropriate ones but my list goes from 19,000 to 4,000 before I drop immune related genes due to a lot of NAs. I tried reactomedb, but the pathnames don't really let me filter by immune related or not.
Any advice is appreciated.
KEGG https://www.genome.jp/kegg/ "KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. See Release notes (April 1, 2022) for new and updated features."