GenomicFeatures: transcriptsByOverlaps – R documentation

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transcriptsByOverlaps

Extract genomic features from a TxDb-like object based on their 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 = -1L, minoverlap = 0L,
                      type = c("any", "start", "end"), ...)
## S4 method for signature 'TxDb'
transcriptsByOverlaps(x, ranges,
                      maxgap = -1L, minoverlap = 0L,
                      type = c("any", "start", "end"),
                      columns = c("tx_id", "tx_name"))

exonsByOverlaps(x, ranges,
                maxgap = -1L, minoverlap = 0L,
                type = c("any", "start", "end"), ...)
## S4 method for signature 'TxDb'
exonsByOverlaps(x, ranges,
                maxgap = -1L, minoverlap = 0L,
                type = c("any", "start", "end"),
                columns = "exon_id")

cdsByOverlaps(x, ranges,
              maxgap = -1L, minoverlap = 0L,
              type = c("any", "start", "end"), ...)
## S4 method for signature 'TxDb'
cdsByOverlaps(x, ranges,
              maxgap = -1L, minoverlap = 0L,
              type = c("any", "start", "end"),
              columns = "cds_id")

Arguments

`x`	A TxDb object.
`ranges`	A GRanges object to restrict the output.
`maxgap,minoverlap,type`	Used in the internal call to `findOverlaps()` to detect overlaps. See `?findOverlaps` in the IRanges package for a description of these arguments.
`...`	Arguments to be passed to or from methods.
`columns`	Columns to include in the output. See `?transcripts` for the possible values.

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.

Value

a GRanges object

Author(s)

P. Aboyoun

Examples

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

GenomicFeatures

Conveniently import and query gene models

v1.42.3

Artistic-2.0

Authors

M. Carlson, H. Pagès, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence, V. Obenchain

Initial release