mapRangesToIds: Map Genomic Ranges to IDs
In Bioconductor/GenomicFeatures: Conveniently import and query gene models

mapRangesToIds

R Documentation

Map Genomic Ranges to IDs

Description

Map Genomic Ranges to IDs

Usage

mapRangesToIds(x, ...)

## S4 method for signature 'TxDb'
mapRangesToIds(x, ranges, type = c("cds", "exon", "tx",
  "gene"), columns = NULL, ...)

Arguments

`x`	Database to use for mapping
`ranges`	range object used to subset
`type`	of feature to return
`columns`	additional metadata columns to include in the output.
`...`	Additional arguments passed to `findOverlaps`

Value

DataFrame of mcols from the database.

Methods (by class)

TxDb: TxDb method

Examples

fl <- system.file(package = "GenomicFeatures", "extdata", "sample_ranges.rds")
txdb <- makeTxDbFromGRanges(readRDS(fl))

keys <- list(tx_name = c("ENST00000371582", "ENST00000371588",
    "ENST00000494752", "ENST00000614008", "ENST00000496771"))
res <- mapIdsToRanges(txdb, keys = keys, type = "tx")
mapRangesToIds(txdb, res, "tx")

Bioconductor/GenomicFeatures documentation built on March 14, 2024, 6:16 a.m.