Extract genomic features from a TxDb-like object
Generic functions to extract genomic features from a TxDb-like object. This page documents the methods for TxDb objects only.
transcripts(x, ...)
## S4 method for signature 'TxDb'
transcripts(x, columns=c("tx_id", "tx_name"), filter=NULL, use.names=FALSE)
exons(x, ...)
## S4 method for signature 'TxDb'
exons(x, columns="exon_id", filter=NULL, use.names=FALSE)
cds(x, ...)
## S4 method for signature 'TxDb'
cds(x, columns="cds_id", filter=NULL, use.names=FALSE)
genes(x, ...)
## S4 method for signature 'TxDb'
genes(x, columns="gene_id", filter=NULL, single.strand.genes.only=TRUE)
## S4 method for signature 'TxDb'
promoters(x, upstream=2000, downstream=200, use.names=TRUE, ...)x |
A TxDb object. |
... |
For the For the |
columns |
Columns to include in the output.
Must be
If the vector is named, those names are used for the corresponding column in the element metadata of the returned object. |
filter |
Either |
use.names |
|
single.strand.genes.only |
If |
upstream |
For |
downstream |
For |
These are the main functions for extracting transcript information
from a TxDb-like object. These methods can restrict the output
based on categorical information. To restrict the output based on interval
information, use the transcriptsByOverlaps,
exonsByOverlaps, and cdsByOverlaps
functions.
The promoters function computes user-defined promoter regions
for the transcripts in a TxDb-like object. The return object is
a GRanges of promoter regions around the transcription start
site the span of which is defined by upstream and downstream.
For additional details on how the promoter range is computed and the
handling of + and - strands see
?`promoters,GRanges-method`.
A GRanges object. The only exception being
when genes is used with single.strand.genes.only=FALSE,
in which case a GRangesList object is returned.
M. Carlson, P. Aboyoun and H. Pagès
transcriptsBy and transcriptsByOverlaps
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 reference 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.
microRNAs and tRNAs for extracting
microRNA or tRNA genomic ranges from a TxDb object.
id2name for mapping TxDb internal ids
to external names for a given feature type.
The TxDb class.
txdb_file <- system.file("extdata", "hg19_knownGene_sample.sqlite",
package="GenomicFeatures")
txdb <- loadDb(txdb_file)
## ---------------------------------------------------------------------
## transcripts()
## ---------------------------------------------------------------------
tx1 <- transcripts(txdb)
tx1
transcripts(txdb, use.names=TRUE)
transcripts(txdb, columns=NULL, use.names=TRUE)
filter <- list(tx_chrom = c("chr3", "chr5"), tx_strand = "+")
tx2 <- transcripts(txdb, filter=filter)
tx2
## Sanity checks:
stopifnot(
identical(mcols(tx1)$tx_id, seq_along(tx1)),
identical(tx2, tx1[seqnames(tx1) == "chr3" & strand(tx1) == "+"])
)
## ---------------------------------------------------------------------
## exons()
## ---------------------------------------------------------------------
exons(txdb, columns=c("EXONID", "TXNAME"),
filter=list(exon_id=1))
exons(txdb, columns=c("EXONID", "TXNAME"),
filter=list(tx_name="uc009vip.1"))
## ---------------------------------------------------------------------
## genes()
## ---------------------------------------------------------------------
genes(txdb) # a GRanges object
cols <- c("tx_id", "tx_chrom", "tx_strand",
"exon_id", "exon_chrom", "exon_strand")
## By default, genes are returned in a GRanges object and those that
## cannot be represented by a single genomic range (because they have
## exons located on both strands of the same reference sequence or on
## more than one reference sequence) are dropped with a message:
single_strand_genes <- genes(txdb, columns=cols)
## Because we've returned single strand genes only, the "tx_chrom"
## and "exon_chrom" metadata columns are guaranteed to match
## 'seqnames(single_strand_genes)':
stopifnot(identical(as.character(seqnames(single_strand_genes)),
as.character(mcols(single_strand_genes)$tx_chrom)))
stopifnot(identical(as.character(seqnames(single_strand_genes)),
as.character(mcols(single_strand_genes)$exon_chrom)))
## and also the "tx_strand" and "exon_strand" metadata columns are
## guaranteed to match 'strand(single_strand_genes)':
stopifnot(identical(as.character(strand(single_strand_genes)),
as.character(mcols(single_strand_genes)$tx_strand)))
stopifnot(identical(as.character(strand(single_strand_genes)),
as.character(mcols(single_strand_genes)$exon_strand)))
all_genes <- genes(txdb, columns=cols, single.strand.genes.only=FALSE)
all_genes # a GRangesList object
multiple_strand_genes <- all_genes[elementNROWS(all_genes) >= 2]
multiple_strand_genes
mcols(multiple_strand_genes)
## ---------------------------------------------------------------------
## promoters()
## ---------------------------------------------------------------------
## This:
promoters(txdb, upstream=100, downstream=50)
## is equivalent to:
promoters(transcripts(txdb, use.names=TRUE), upstream=100, downstream=50)
## Extra arguments are passed to transcripts(). So this:
columns <- c("tx_name", "gene_id")
promoters(txdb, upstream=100, downstream=50, columns=columns)
## is equivalent to:
promoters(transcripts(txdb, columns=columns, use.names=TRUE),
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