gene2go: A function that map Gene IDs to GO terms (including the...

In ZhenWei10/golite: Fast and simple GOEA

Usage

gene2go(Gene_ID, Gene_key_type = "ENTREZID", OrgDB, Category = "BP",
  Drop_zero_match = F, Slim = F, Slim_subset = NULL,
  Exclude_self_slim = T)

Arguments

Gene_ID	gene ids to query.
Gene_key_type	a character specifying the type of the ID, the available types of the keys can be find using keytypes(org.Hs.eg.db), default "ENTREZID".
OrgDB	an OrgDb object defined by AnnotationDbi.
Category	a character specifying the gene ontology category, can be one in "BP", "CC", and "MF", default "BP".
Drop_zero_match	whether to drop the genes that mapped to no terms at all, default FALSE.
Slim	Wheather to return a mapping to GO slim terms (a certain subset to GO terms), default FALSE.
Slim_subset	A character sting of GO terms that define the scope of GO Slim. if not provided, the GO slim would be the generic subset defined in : http://geneontology.org/ontology/subsets/goslim_generic.obo
Exclude_self_slim	whether the GO slim terms of its own category i.e. remove terms of c("GO:0008150","GO:0005575","GO:0003674").

Value

a data.frame that define the mapping relationship between genes and GO terms.

ZhenWei10/golite documentation built on May 30, 2019, 6:15 p.m.