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Filter Foreground and Background ID Sets by Gene Type

Source: R/poolFilter.R
poolFilter.Rd

poolFilter() takes the mapped foreground and background ID data frames (as produced by mapIDs()) and, if requested, filters both sets to only include genes (or their transcripts) of a specified biotype (e.g. “protein-coding”).

Usage

poolFilter(mapped, geneType = NULL)

Arguments

mapped

A list returned by mapIDs(), containing at least:

  • fg_ids: data.frame with columns entrez and mappedID (foreground).

  • bg_ids: data.frame with columns entrez and mappedID (background).

  • so_obj: a src_organism object for transcript lookups.

  • orgdb: the loaded OrgDb package object.

  • transcript: logical, whether IDs are transcripts.

geneType

Optional character scalar; if not NULL, only genes of this biotype (GENETYPE in the OrgDb) will be retained. Valid values vary by organism (e.g. “protein-coding”, “lncRNA”, etc.).

Value

The original mapped list, but with fg_ids and bg_ids replaced by filtered versions (only rows matching geneType, if provided).

Examples

library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(org.Hs.eg.db)

txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
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
filtered <- poolFilter(ids, geneType="protein-coding")