GenomicFeatures (version 1.24.4)

transcriptsByOverlaps: Extract genomic features from an object based on their by genomic location

Description

Generic functions to extract genomic features for specified genomic locations. This page documents the methods for TxDb objects only.

Usage

transcriptsByOverlaps(x, ranges, maxgap = 0L, minoverlap = 1L, type = c("any", "start", "end"), ...)
"transcriptsByOverlaps"(x, ranges, maxgap = 0L, minoverlap = 1L, type = c("any", "start", "end"), columns = c("tx_id", "tx_name"))
exonsByOverlaps(x, ranges, maxgap = 0L, minoverlap = 1L, type = c("any", "start", "end"), ...)
"exonsByOverlaps"(x, ranges, maxgap = 0L, minoverlap = 1L, type = c("any", "start", "end"), columns = "exon_id")
cdsByOverlaps(x, ranges, maxgap = 0L, minoverlap = 1L, type = c("any", "start", "end"), ...)
"cdsByOverlaps"(x, ranges, maxgap = 0L, minoverlap = 1L, type = c("any", "start", "end"), columns = "cds_id")

Arguments

x

A TxDb object.

...

Arguments to be passed to or from methods.

ranges

A GRanges object to restrict the output.

type

How to perform the interval overlap operations of the ranges. See the findOverlaps manual page in the GRanges package for more information.

maxgap

A non-negative integer representing the maximum distance between a query interval and a subject interval.

minoverlap

Ignored.

columns

Columns to include in the output. See ?transcripts for the possible values.

Value

Details

These functions subset the results of transcripts, exons, and cds function calls with using the results of findOverlaps calls based on the specified ranges.

See Also

• transcripts and transcriptsBy for more ways to extract genomic features from a TxDb object.
• select-methods for how to use the simple "select" interface to extract information from a TxDb object.
• id2name for mapping TxDb internal ids to external names for a given feature type.
• The TxDb class.

Examples

  txdb <- loadDb(system.file("extdata", "hg19_knownGene_sample.sqlite",
                                   package="GenomicFeatures"))
  gr <- GRanges(seqnames = rep("chr1",2),
                ranges = IRanges(start=c(500,10500), end=c(10000,30000)),
                strand = strand(rep("-",2)))
  transcriptsByOverlaps(txdb, gr)