transcriptsByOverlaps: Extract genomic features from a TxDb-like object based on...

In Bioconductor/GenomicFeatures: Query the gene models of a given organism/assembly

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

See Also

• transcripts and transcriptsBy for more ways to extract genomic features from a TxDb-like object.

• transcriptLengths for extracting the transcript lengths (and other metrics) from a TxDb object.

• exonicParts and intronicParts for extracting non-overlapping exonic or intronic parts from a TxDb-like object.

• extractTranscriptSeqs for extracting transcript (or CDS) sequences from chromosome sequences.

• coverageByTranscript for computing coverage by transcript (or CDS) of a set of ranges.

• 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(Rle("chr1", 2),
              IRanges(c(500,10500), c(10000,30000)),
              strand = Rle("-", 2))
transcriptsByOverlaps(txdb, gr)

Bioconductor/GenomicFeatures documentation built on Nov. 7, 2024, 4:25 a.m.