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

Description Usage Arguments Value Examples

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

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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

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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)

BiocSet documentation built on Nov. 8, 2020, 7:48 p.m.