Extract and group genomic features of a given type from a TxDb-like object
Generic functions to extract genomic features of a given type grouped based on another type of genomic feature. This page documents the methods for TxDb objects only.
transcriptsBy(x, by=c("gene", "exon", "cds"), ...)
## S4 method for signature 'TxDb'
transcriptsBy(x, by=c("gene", "exon", "cds"), use.names=FALSE)
exonsBy(x, by=c("tx", "gene"), ...)
## S4 method for signature 'TxDb'
exonsBy(x, by=c("tx", "gene"), use.names=FALSE)
cdsBy(x, by=c("tx", "gene"), ...)
## S4 method for signature 'TxDb'
cdsBy(x, by=c("tx", "gene"), use.names=FALSE)
intronsByTranscript(x, ...)
## S4 method for signature 'TxDb'
intronsByTranscript(x, use.names=FALSE)
fiveUTRsByTranscript(x, ...)
## S4 method for signature 'TxDb'
fiveUTRsByTranscript(x, use.names=FALSE)
threeUTRsByTranscript(x, ...)
## S4 method for signature 'TxDb'
threeUTRsByTranscript(x, use.names=FALSE)x |
A TxDb object. |
... |
Arguments to be passed to or from methods. |
by |
One of |
use.names |
Controls how to set the names of the returned
GRangesList object.
These functions return all the features of a given type (e.g.
all the exons) grouped by another feature type (e.g. grouped by
transcript) in a GRangesList object.
By default (i.e. if Finally, |
These functions return a GRangesList object where the ranges within each of the elements are ordered according to the following rule:
When using exonsBy or cdsBy with by = "tx",
the returned exons or CDS are ordered by ascending rank for each
transcript, that is, by their position in the transcript.
In all other cases, the ranges will be ordered by chromosome, strand,
start, and end values.
A GRangesList object.
M. Carlson, P. Aboyoun and H. Pagès
transcripts 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 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.
txdb_file <- system.file("extdata", "hg19_knownGene_sample.sqlite",
package="GenomicFeatures")
txdb <- loadDb(txdb_file)
## Get the transcripts grouped by gene:
transcriptsBy(txdb, "gene")
## Get the exons grouped by gene:
exonsBy(txdb, "gene")
## Get the CDS grouped by transcript:
cds_by_tx0 <- cdsBy(txdb, "tx")
## With more informative group names:
cds_by_tx1 <- cdsBy(txdb, "tx", use.names=TRUE)
## Note that 'cds_by_tx1' can also be obtained with:
names(cds_by_tx0) <- id2name(txdb, feature.type="tx")[names(cds_by_tx0)]
stopifnot(identical(cds_by_tx0, cds_by_tx1))
## Get the introns grouped by transcript:
intronsByTranscript(txdb)
## Get the 5' UTRs grouped by transcript:
fiveUTRsByTranscript(txdb)
fiveUTRsByTranscript(txdb, use.names=TRUE) # more informative group namesPlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.