mapping_set {BiocSet} | R Documentation

## 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)

[Package BiocSet version 1.1.2 Index]