mapping_element: Functions for mapping elements in the element tibble to...

In Bioconductor/BiocSet: Representing Different Biological Sets

Functions for mapping elements in the element tibble to different id types

Description

Functions for dealing with unique mapping and multiple mapping. map_add_element will add the mapping as a new column instead of overwriting the current one used for the mapping.

Usage

map_unique(es, org, from, to)

map_multiple(
  es,
  org,
  from,
  to,
  multi = c("list", "filter", "asNA", "CharacterList")
)

map_add_element(es, org, from, add)

Arguments

es	The BiocSet objec to map the elements on.
org	The AnnotationDbi object to identify keys/mappings from.
from	A character to indicate which identifier to map from.
to	A character to indicate which identifier to map to.
multi	How should multiple values be returned? Options include: list: This will just return a list object to the end user. filter: This will remove all elements that contain multiple matches and will therefore return a shorter vector than what came in whenever some of the keys match more than one value. asNA: This will return an NA value whenever there are multiple matches. CharacterList: This just returns a SimpleCharacterList object. FUN: A function can be supplied to the 'multiVals' argument for custom behaviors.
add	The id to add to the BiocSet object.

Value

For map_unique, a BiocSet object with unique elements.

For map_multiple, a BiocSet object with multiple mappings for certain elements.

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

Examples

library(org.Hs.eg.db)
es <- BiocSet(set1 = c("C5", "GANC"), set2 = c("AFM", "CGB1", "ADAM32"))
map_unique(es, org.Hs.eg.db, "SYMBOL", "ENTREZID")

map_multiple(es, org.Hs.eg.db, "SYMBOL", "ENSEMBLTRANS", "asNA")

map <- map_add_element(es, org.Hs.eg.db, "SYMBOL", "ENTREZID")
es %>% mutate_element(entrez = map)

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