pipeTopGO: Run gene ontology enrichment analyses

In jtlovell/RNAseqDE: A pipeline for differential expression analyses in R

Description

pipeTopGO Methods to simplify running limma::topGO from a table-like GO annotation database.

Usage

pipeTopGO(genes.of.interest, GO.db, GO.db.colname = "GO",
  GO.db.geneIDs = "geneID", GO.db.sep = ",", min.n.annot = 0,
  cull2genes = NULL, output = "culled")

Arguments

genes.of.interest	A character vector representing the genes that are to be tested.
GO.db	The GO database in tabular format. One column must contain the unique gene identifier. Gene IDs must not be replicated. Multiple GO terms must be separated by comma (or similar) in a single dataframe column.
GO.db.colname	The name of the column that contains the GO terms
GO.db.geneIDs	The name of the GO.db column that contains the unique gene identifier
GO.db.sep	The character that separates GO terms.
cull2genes	Specify if the background to test should be a gene set other than the entire GO database
output	Should the output be culled so that GO terms with P values equal to 1 are not returned.

Details

More here soon.

Value

A tabular presentation of GO terms and the resulting statistics

jtlovell/RNAseqDE documentation built on May 10, 2019, 8:06 a.m.