get_anno_categories: Get all associated ontology categories for the input genes

In GOfuncR: Gene ontology enrichment using FUNC

Description

Returns all associated GO-categories given a vector of gene-symbols, e.g. c('SPAG5', 'BTC').

Usage

get_anno_categories(genes,  database = 'Homo.sapiens', annotations = NULL,
    term_df = NULL, godir = NULL, silent = FALSE)

Arguments

genes	a character() vector of gene-symbols, e.g. c('SPAG5', 'BTC').
database	optional character() defining an OrganismDb or OrgDb annotation package from Bioconductor, like 'Mus.musculus' (mouse) or 'org.Pt.eg.db' (chimp).
annotations	optional data.frame() with two character() columns: gene-symbols and GO-categories. Alternative to 'database'.
term_df	optional data.frame() with an ontology 'term' table. Alternative to the default integrated GO-graph or godir.
godir	optional character() specifying a directory that contains the ontology table 'term.txt'. Alternative to the default integrated GO-graph or term_df.
silent	logical. If TRUE all output to the screen except for warnings and errors is suppressed.

Details

Besides the default 'Homo.sapiens', also other OrganismDb or OrgDb packages from Bioconductor, like 'Mus.musculus' (mouse) or 'org.Pt.eg.db' (chimp), can be used. It is also possible to directly provide a dataframe with annotations, which is then searched for the input genes and filtered for GO-categories that are present in the ontology.

By default the package's integrated ontology is used, but a custom ontology can be defined, too. For details on how to use a custom ontology with term_df or godir please refer to the package's vignette. The advantage of term_df over godir is that the latter reads the file 'term.txt' from disk and therefore takes longer.

Value

a data.frame() with four columns: gene (character()), GO-ID (character(), GO-name (character() and GO-domain (character()).

Note

This gives only direct annotations of genes to GO-categories. By definition genes are also indirectly annotated to all parent nodes of those categories. Use get_parent_nodes to get the higher level categories of the directly annotated GO-categories.
Also note that GO-categories which are not represented or obsolete in the internal GO-graph of GOfuncR or the custom ontology provided through term_df or godir are removed to be consistent with the annotations used in go_enrich.

Author(s)

Steffi Grote

References

[1] Ashburner, M. et al. (2000). Gene Ontology: tool for the unification of biology. Nature Genetics 25, 25-29.

See Also

get_anno_genes
get_parent_nodes
get_names

Examples

## get the GO-annotations for two random genes
anno1 = get_anno_categories(c('BTC', 'SPAG5'))
head(anno1)

GOfuncR documentation built on Nov. 8, 2020, 8:27 p.m.