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Map User IDs to Entrez and Determine Best Keytype

Source: R/mapIDs.R
mapIDs.Rd

Given a vector of user-supplied gene/transcript IDs, finds the AnnotationDbi keytype (e.g. ens, refseq, symbol, etc.) that maps the highest fraction of inputs, and returns both foreground and full background sets as Entrez IDs. Optionally collapses transcript-style inputs to genes when requested or when reverse-mapping inflation exceeds a threshold.

Usage

mapIDs(
  orgdb,
  id_type,
  foreground_ids,
  background_ids = NULL,
  threshold = 0.9,
  transcript = FALSE,
  stripVersions = TRUE,
  inflateThresh = 1
)

Arguments

orgdb

An OrgDb object. (e.g. org.Hs.eg.db).

id_type

Type of identifier supplied in foreground and background IDs.

foreground_ids

Character vector of gene or transcript IDs (e.g. Ensembl, RefSeq, gene symbols) to analyze.

background_ids

Character vector of gene or transcript IDs to use as background set.

threshold

Fraction in range 0 to 1; minimum mapping rate to accept a keytype without falling back (default 0.9).

transcript

Logical; if TRUE, analyze as transcript-level IDs (default FALSE).

stripVersions

Logical; strip version suffixes (e.g. ".1") from Ensembl/RefSeq IDs.

inflateThresh

Fraction in range 0 to 1; if reverse-mapping shows excessive, inflation automatically collapse transcripts to genes (default 1 ie. 100%).

Value

A named list combining the original mapping components with:

fg_ids

data.frame(entrez, mappedID) for your foreground set

bg_ids

data.frame(entrez, mappedID) for the full background

userIDtype

the chosen keytype (e.g. "ensembl")

transcript

logical, whether transcript-level mapping was used

Examples

library(org.Hs.eg.db)
orgdb <- org.Hs.eg.db

my_genes <- c("ENSG00000139618", "ENSG00000157764")
ids <- mapIDs(orgdb = orgdb, 
              foreground_ids = my_genes, 
              id_type = "ENSEMBL")
#> Mapping foreground ids to ENTREZIDs...
#> 'select()' returned 1:1 mapping between keys and columns
#> Successfully mapped 100% of the provided foreground ids.
#> Building background id set...
#> 'select()' returned 1:many mapping between keys and columns
#> Checking for inflation...
#> 'select()' returned 1:1 mapping between keys and columns
  
# Transcript Ids
my_transcripts <- c("ENST00000245479", "ENST00000633194")
ids <- mapIDs(orgdb = orgdb,
              foreground_ids = my_transcripts,
              id_type = "ENSEMBLTRANS",
              transcript = TRUE)
#> Mapping foreground ids to ENTREZIDs...
#> 'select()' returned 1:1 mapping between keys and columns
#> Successfully mapped 100% of the provided foreground ids.
#> Building background id set...
#> 'select()' returned 1:many mapping between keys and columns