transcriptLengths: Extract the transcript lengths (and other metrics) from a...
In jmacdon/GenomicFeatures: Conveniently import and query gene models

Description Usage Arguments Details Value Author(s) See Also Examples

The transcriptLengths function extracts the transcript lengths from a TxDb object. It also returns the CDS and UTR lengths for each transcript if the user requests them.

1 2	transcriptLengths(txdb, with.cds_len=FALSE, with.utr5_len=FALSE, with.utr3_len=FALSE, ...)

`txdb`	A TxDb object.
`with.cds_len, with.utr5_len, with.utr3_len`	`TRUE` or `FALSE`. Whether or not to also extract and return the CDS, 5' UTR, and 3' UTR lengths for each transcript.
`...`	Additional arguments used by `transcripts` and other accessor functions.

All the lengths are counted in number of nucleotides.

The length of a processed transcript is just the sum of the lengths of its exons. This should not be confounded with the length of the stretch of DNA transcribed into RNA (a.k.a. transcription unit), which can be obtained with width(transcripts(txdb)).

A data frame with 1 row per transcript. The rows are guaranteed to be in the same order as the elements of the GRanges object returned by transcripts(txdb). The data frame has between 5 and 8 columns, depending on what the user requested via the with.cds_len, with.utr5_len, and with.utr3_len arguments.

The first 3 columns are the same as the metadata columns of the object returned by

1	transcripts(txdb, columns=c("tx_id", "tx_name", "gene_id"))

that is:

tx_id: The internal transcript ID. This ID is unique within the scope of the TxDb object. It is not an official or public ID (like an Ensembl or FlyBase ID) or an Accession number, so it cannot be used to lookup the transcript in public data bases or in other TxDb objects. Furthermore, this ID could change when re-running the code that was used to make the TxDb object.
tx_name: An official/public transcript name or ID that can be used to lookup the transcript in public data bases or in other TxDb objects. This column is not guaranteed to contain unique values and it can contain NAs.
gene_id: The official/public ID of the gene that the transcript belongs to. Can be NA if the gene is unknown or if the transcript is not considered to belong to a gene.

The other columns are quantitative:

nexon: The number of exons in the transcript.
tx_len: The length of the processed transcript.
cds_len: [optional] The length of the CDS region of the processed transcript.
utr5_len: [optional] The length of the 5' UTR region of the processed transcript.
utr3_len: [optional] The length of the 3' UTR region of the processed transcript.

Hervé Pagès

transcripts, transcriptsBy, and transcriptsByOverlaps, for extracting genomic feature locations from a TxDb-like 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.
makeTxDbFromUCSC, makeTxDbFromBiomart, and makeTxDbFromEnsembl, for making a TxDb object from online resources.
makeTxDbFromGRanges and makeTxDbFromGFF for making a TxDb object from a GRanges object, or from a GFF or GTF file.
The TxDb class.

library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene
dm3_txlens <- transcriptLengths(txdb)
head(dm3_txlens)

dm3_txlens <- transcriptLengths(txdb, with.cds_len=TRUE,
                                      with.utr5_len=TRUE,
                                      with.utr3_len=TRUE)
head(dm3_txlens)

## When cds_len is 0 (non-coding transcript), utr5_len and utr3_len
## must also be 0:
non_coding <- dm3_txlens[dm3_txlens$cds_len == 0, ]
stopifnot(all(non_coding[6:8] == 0))

## When cds_len is not 0 (coding transcript), cds_len + utr5_len +
## utr3_len must be equal to tx_len:
coding <- dm3_txlens[dm3_txlens$cds_len != 0, ]
stopifnot(all(rowSums(coding[6:8]) == coding[[5]]))

## A sanity check:
stopifnot(identical(dm3_txlens$tx_id, mcols(transcripts(txdb))$tx_id))