| transcriptsByOverlaps {GenomicFeatures} | R Documentation |
Generic functions to extract genomic features for specified genomic locations. This page documents the methods for TranscriptDb objects only.
transcriptsByOverlaps(x, ranges,
maxgap = 0L, minoverlap = 1L,
type = c("any", "start", "end"), ...)
## S4 method for signature 'TranscriptDb'
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"), ...)
## S4 method for signature 'TranscriptDb'
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"), ...)
## S4 method for signature 'TranscriptDb'
cdsByOverlaps(x, ranges,
maxgap = 0L, minoverlap = 1L,
type = c("any", "start", "end"),
columns = "cds_id")
x |
A TranscriptDb 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
|
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 |
These functions subset the results of transcripts,
exons, and cds function calls with
using the results of findOverlaps
calls based on the specified ranges.
a GRanges object
P. Aboyoun
txdb <- loadFeatures(system.file("extdata", "UCSC_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)