mkEnrich: Make Gene Ontology Enrichment Object

In genejockey33000/typGumbo: Scripts and Pipelines for RNAseq Analysis

Make Gene Ontology Enrichment Object

Description

Simple script that uses clusterProfiler to generate GO enrichment object. Takes single column .csv file of gene symbols (i.e. "MAPT", "NEUROG2") as input (no column header). Outputted object can be fed into downstream functions like gene concept network plots Can take a bit of time to run.

Usage

mkEnrich(x, db = "GO", GOont = "ALL", qvalueCutoff = 0.01)

Arguments

x	quoted path to *.csv file containing ONE column of gene names
db	One of "GO" (default), or "MKEGG". May add more later but Reactome is being problematic.
GOont	Enter one of "ALL" (default), "BP", "MF", "CC"
qvalueCutoff	Highest qvalue returned (default = .01)

Value

GO enrichment object

genejockey33000/typGumbo documentation built on July 20, 2023, 11:45 p.m.