TranscriptDb-class {GenomicFeatures} | R Documentation |
The TranscriptDb class is a container for storing transcript annotations.
See ?FeatureDb
for a more generic container for storing
genomic locations of an arbitrary type of genomic features.
See ?makeTranscriptDbFromUCSC
and
?makeTranscriptDbFromBiomart
for convenient ways to
make TranscriptDb objects from UCSC or BioMart online resources.
See ?makeTranscriptDbFromGFF
for making a TranscriptDb
object from annotations available as a GFF3 or GTF file.
In the code snippets below, x
is a TranscriptDb object.
metadata(x)
:
Return x
's metadata in a data frame.
seqinfo(x)
, seqinfo(x) <- value
:
Get or set the information about the underlying sequences.
Note that, for now, the setter only supports replacement of the
sequence names, i.e., except for their sequence names (accessed with
seqnames(value)
and seqnames(seqinfo(x))
, respectively),
Seqinfo objects value
(supplied) and
seqinfo(x)
(current) must be identical.
isActiveSeq(x)
:
Return the currently active sequences for this txdb object as a
named logical vector. Only active sequences will be tapped when
using the supplied accessor methods. Inactive sequences will be
ignored. By default, all available sequences will be active.
isActiveSeq(x) <- value
:
Allows the user to change which sequences will be actively
accessed by the accessor methods by altering the contents of this
named logical vector.
seqnameStyle(x)
:
List the matching seqname styles for x
.
seqnameStyle(x)
is equivalent to seqnameStyle(seqinfo(x))
.
Note that this information is not stored in x
but inferred
by looking up seqlevels(x)
against a seqname style database
stored in the seqnames.db metadata package (required).
determineDefaultSeqnameStyle(x)
:
Determine the default seqname style for the database in x
.
as.list(x)
:
Dumps the entire db into a list of data frames txdump
that can
be used in do.call(makeTranscriptDb, txdump)
to make the db
again with no loss of information.
Note that the transcripts are dumped in the same order in all the
data frames.
H. Pages, Marc Carlson
The FeatureDb class for storing genomic locations of an arbitrary type of genomic features.
makeTranscriptDbFromUCSC
and
makeTranscriptDbFromBiomart
for convenient ways to
make TranscriptDb objects from UCSC or BioMart online resources.
makeTranscriptDbFromGFF
for making a TranscriptDb
object from annotations available as a GFF3 or GTF file.
saveDb
and loadDb
for
saving and loading the database content of a TranscriptDb object.
transcripts
, transcriptsBy
,
and transcriptsByOverlaps
,
for how to extract genomic features from a TranscriptDb object.
select-methods for how to use the simple "select" interface to extract information from a TranscriptDb object.
The Seqinfo class in the GenomicRanges package.
txdb_file <- system.file("extdata", "Biomart_Ensembl_sample.sqlite", package="GenomicFeatures") txdb <- loadDb(txdb_file) txdb ## Use of seqinfo seqinfo(txdb) seqlevels(txdb) # shortcut for 'seqlevels(seqinfo(txdb))' seqlengths(txdb) # shortcut for 'seqlengths(seqinfo(txdb))' isCircular(txdb) # shortcut for 'isCircular(seqinfo(txdb))' names(which(isCircular(txdb))) ## Can set txdb so that only chr1 and chr2 are used by using the seqlevels seqlevels(txdb, force=TRUE) <- c("1", "2") ## And then you can restore the default seqlevels txdb <- restoreSeqlevels(txdb) ## Use of as.list txdump <- as.list(txdb) txdump txdb1 <- do.call(makeTranscriptDb, txdump) stopifnot(identical(as.list(txdb1), txdump))