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