mapRangesToIds: Map Genomic Ranges to IDs

In jmacdon/GenomicFeatures: Conveniently import and query gene models

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")

jmacdon/GenomicFeatures documentation built on Jan. 2, 2022, 7:40 a.m.