IDToGO: IDToGO

In astatham/GOfish: Fishing for GO terms? SO ARE WE!

Description

IDToGO

Usage

IDToGO(ids, universe=NULL, ontology=c("BP", "MF", "CC"), ID=c("entrez", "genbank", "alias", "ensembl", "symbol", "genename", "unigene"), speciesdb=c("org.Mm.eg.db", "org.Hs.eg.db"), n=NULL, p.adj=NULL, p.cutoff=0.05, orderBy=c("classic", "elim", "parentchild"), tests=NULL)

Arguments

ids	List of IDs to test for GO term enrichments
universe	List of IDs to use as the background. If NULL then use all IDs listed in the speciesdb
ontology	Which ontology to test
ID	Which type of ID - passed into annFUN
speciesdb	Which species database to use
n	How many GO terms to return after ordering. If 0 return all hits, if NULL n is chosen by the p value cutoff specified by p.cutoff
p.adj	Which method of p value adjustment for multiple testing to use - for details see help("p.adjust"). Ignored if n is specified.
p.cutoff	What p value cutoff to use when reporting significant GO terms. Ignored if n is specified.
orderBy	Which of the 3 testing algorithms to order the results in the table by. This algorithms p value is the one used as a p value cutoff when n is NULL.
tests	Which of the 3 testing algorithms to use (and return the results of) in addition to the one chosen in orderBy.

Value

Good question

Author(s)

Aaron Statham

astatham/GOfish documentation built on May 10, 2019, 2:05 p.m.