makeTranscriptDbFromUCSC {GenomicFeatures} | R Documentation |
The makeTranscriptDbFromUCSC
function allows the user
to make a TranscriptDb object from transcript annotations
available at the UCSC Genome Browser.
supportedUCSCtables() getChromInfoFromUCSC( genome, goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath") makeTranscriptDbFromUCSC( genome="hg18", 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 TranscriptDb 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 |
makeTranscriptDbFromUCSC
is a convenience function that feeds
data from the UCSC source to the lower level makeTranscriptDb
function.
See ?makeTranscriptDbFromBiomart
for a similar function
that feeds data from a BioMart database.
A TranscriptDb object.
M. Carlson and H. Pages
ucscGenomes
,
DEFAULT_CIRC_SEQS
,
makeTranscriptDbFromBiomart
,
makeTranscriptDbFromGFF
,
makeTranscriptDb
,
supportedMiRBaseBuildValues
## Display the list of genomes available at UCSC: library(rtracklayer) ucscGenomes()[ , "db"] ## Display the list of tables supported by makeTranscriptDbFromUCSC(): supportedUCSCtables() ## Not run: ## Retrieving a full transcript dataset for Yeast from UCSC: txdb1 <- makeTranscriptDbFromUCSC(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 <- makeTranscriptDbFromUCSC(genome="mm9", tablename="knownGene", transcript_ids=transcript_ids) txdb2