| makeTxDbFromUCSC {GenomicFeatures} | R Documentation |
The makeTxDbFromUCSC function allows the user
to make a TxDb object from transcript annotations
available at the UCSC Genome Browser.
supportedUCSCtables()
getChromInfoFromUCSC(
genome,
goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath")
makeTxDbFromUCSC(
genome="hg19",
tablename="knownGene",
transcript_ids=NULL,
circ_seqs=DEFAULT_CIRC_SEQS,
url="http://genome.ucsc.edu/cgi-bin/",
goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath",
miRBaseBuild=NA)
genome |
genome abbreviation used by UCSC and obtained by
|
tablename |
name of the UCSC table containing the transcript
annotations to retrieve. Use the |
transcript_ids |
optionally, only retrieve transcript annotation data for the specified set of transcript ids. If this is used, then the meta information displayed for the resulting TxDb object will say 'Full dataset: no'. Otherwise it will say 'Full dataset: yes'. |
circ_seqs |
a character vector to list out which chromosomes should be marked as circular. |
url,goldenPath_url |
use to specify the location of an alternate UCSC Genome Browser. |
miRBaseBuild |
specify the string for the appropriate build
Information from mirbase.db to use for microRNAs. This can be
learned by calling |
makeTxDbFromUCSC is a convenience function that feeds
data from the UCSC source to the lower level makeTxDb
function.
See ?makeTxDbFromBiomart for a similar function
that feeds data from a BioMart database.
A TxDb object.
M. Carlson and H. Pages
makeTxDbFromBiomart, makeTxDbFromGRanges,
and makeTxDbFromGFF, for convenient ways to make a
TxDb object from BioMart online resources, or from a
GRanges object, or from a GFF or GTF file.
ucscGenomes in the rtracklayer
package.
The supportedMiRBaseBuildValues function for
listing all the possible values for the miRBaseBuild
argument.
The TxDb class.
makeTxDb for the low-level function used by the
makeTxDbFrom* functions to make the TxDb object
returned to the user.
## Display the list of genomes available at UCSC:
library(rtracklayer)
ucscGenomes()[ , "db"]
## Display the list of tables supported by makeTxDbFromUCSC():
supportedUCSCtables()
## Not run:
## Retrieving a full transcript dataset for Yeast from UCSC:
txdb1 <- makeTxDbFromUCSC(genome="sacCer2", tablename="ensGene")
## End(Not run)
## Retrieving an incomplete transcript dataset for Mouse from UCSC
## (only transcripts linked to Entrez Gene ID 22290):
transcript_ids <- c(
"uc009uzf.1",
"uc009uzg.1",
"uc009uzh.1",
"uc009uzi.1",
"uc009uzj.1"
)
txdb2 <- makeTxDbFromUCSC(genome="mm9", tablename="knownGene",
transcript_ids=transcript_ids)
txdb2