mapping_set: Functions for mapping sets in the set tibble to different id...

In Bioconductor/BiocSet: Representing Different Biological Sets

Functions for mapping sets in the set tibble to different id types

Description

Functions for creating BiocSet objects from GO sets and KEGG sets, and creating a new set mapping from a current BiocSet object. map_add_set will add the mapping as a new column instead of overwriting the current one used for the mapping.

Usage

go_sets(org, from, go = c("GO", "GOID"), evidence = NULL, ontology = NULL)

kegg_sets(species)

map_set(.data, from, to)

map_add_set(.data, org, from, add)

Arguments

org	The AnnotationDbi object to identify keys/mappings from.
from	A character to indicate which identifier to map from.
go	A character to indicate the column name for the GO ids. Default is "GO".
evidence	A character to indicate the evidence codes for GO associations with a gene of interest. Default is all possible evidence codes.
ontology	A character to indicate which Gene Ontology to use. Default is BP, CC, and MF.
species	Which species the pathways are from.
.data	The BiocSet object that contains the set tibble being mapped.
to	A character to indicate which identifier to map to.
add	The id to add to the BiocSet object.

Value

For go_sets, a BiocSet object with GO ids as the set ids.

For kegg_sets, a BiocSet object with Entrez IDs reported as elements (default from KEGGREST) and KEGG pathways as sets.

For map_set, a BiocSet object with the mapped set present in the set tibble.

For map_add_set, a BiocSet object with a new column in the set tibble with the mapping of the new id type.

Examples

library(org.Hs.eg.db)
go <- go_sets(org.Hs.eg.db, "ENSEMBL")

kegg_sets("hsa")

es <- BiocSet(set1 = letters, set2 = LETTERS)
es %>% map_set("set1", "foo") 

library(GO.db)
map <- map_add_set(go, GO.db, "GOID", "DEFINITION")
go %>% mutate_set(definition = map)

Bioconductor/BiocSet documentation built on Oct. 31, 2024, 11:43 p.m.