topGO_wrapper: Wrapper for TopGO - GO term enrichment analysis

In Jtrachsel/funfuns: Functions I Use (Title Case)

Description

Wrapper for TopGO - GO term enrichment analysis

Usage

topGO_wrapper(
  myInterestingGenes,
  mapping_file,
  ont = "BP",
  algor = "elim",
  statistic = "Fisher",
  nodeSize = 10,
  return_GOdata = F
)

Arguments

myInterestingGenes	A vector of genes of interest
mapping_file	a two column file, first column is the gene_ID, second column is a comma delimited list of GO terms associated with that gene
ont	Which GO ontology to use? options are: 'BP', 'MF', 'CC'
algor	What algorithm to use? default is 'elim'
statistic	what test statistic to use? default is 'Fisher'
nodeSize	used to filter rare GO terms, default is 5. Rare GO terms will often show up as significant as an artifact of the test methodology
return_GOdata	logical, if TRUE, the function returns a list of 2. the first is the normal results data frame, the second in the GOdata objects

Value

Returns a dataframe tests for all GO terms in your data. You need to filter based on a reasonable pvalue

Examples

#none yet

Jtrachsel/funfuns documentation built on Aug. 8, 2021, 7:31 p.m.