transcriptsBy: Extract and group genomic features of a given type

Description

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.

Usage

transcriptsBy(x, by=c("gene", "exon", "cds"), ...)
"transcriptsBy"(x, by=c("gene", "exon", "cds"), use.names=FALSE)
exonsBy(x, by=c("tx", "gene"), ...)
"exonsBy"(x, by=c("tx", "gene"), use.names=FALSE)
cdsBy(x, by=c("tx", "gene"), ...)
"cdsBy"(x, by=c("tx", "gene"), use.names=FALSE)
intronsByTranscript(x, ...)
"intronsByTranscript"(x, use.names=FALSE)
fiveUTRsByTranscript(x, ...)
"fiveUTRsByTranscript"(x, use.names=FALSE)
threeUTRsByTranscript(x, ...)
"threeUTRsByTranscript"(x, use.names=FALSE)

Arguments

A TxDb object.

...

Arguments to be passed to or from methods.

One of "gene", "exon", "cds" or "tx". Determines the grouping.

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 use.names is FALSE), the names of this GRangesList object (aka the group names) are the internal ids of the features used for grouping (aka the grouping features), which are guaranteed to be unique. If use.names is TRUE, then the names of the grouping features are used instead of their internal ids. For example, when grouping by transcript (by="tx"), the default group names are the transcript internal ids ("tx_id"). But, if use.names=TRUE, the group names are the transcript names ("tx_name"). Note that, unlike the feature ids, the feature names are not guaranteed to be unique or even defined (they could be all NAs). A warning is issued when this happens. See ?id2name for more information about feature internal ids and feature external names and how to map the formers to the latters.

Finally, use.names=TRUE cannot be used when grouping by gene by="gene". This is because, unlike for the other features, the gene ids are external ids (e.g. Entrez Gene or Ensembl ids) so the db doesn't have a "gene_name" column for storing alternate gene names.

Value

GRangesList object.

Details

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.

Examples

Run this code

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 names

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