Extract the transcript lengths (and other metrics) from a TxDb object
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.
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 |
|
... |
Additional arguments used by |
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
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))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.