makeTxDbFromEnsembl {GenomicFeatures} | R Documentation |
The makeTxDbFromEnsembl
function creates a TxDb object for
a given organism by importing the genomic locations of its transcripts,
exons, CDS, and genes from an Ensembl database.
makeTxDbFromEnsembl(organism="Homo sapiens", release=NA, circ_seqs=DEFAULT_CIRC_SEQS, server="ensembldb.ensembl.org")
organism |
The scientific name (i.e. genus and species, or genus and species
and subspecies) of the organism for which to import the data.
Case is not sensitive. Underscores can be used instead of white spaces
e.g. |
release |
The Ensembl release to query e.g. 89. If set to |
circ_seqs |
A character vector to list out which chromosomes should be marked as circular. |
server |
The name of the MySQL server to query. See https://www.ensembl.org/info/data/mysql.html for the list of Ensembl public MySQL servers. Make sure to use the server nearest to you. It can make a big difference! |
A TxDb object.
makeTxDbFromEnsembl
tends to be faster and more reliable than
makeTxDbFromBiomart
.
H. Pagès
makeTxDbFromUCSC
and makeTxDbFromBiomart
for making a TxDb object from other online resources.
makeTxDbFromGRanges
and makeTxDbFromGFF
for making a TxDb object from a GRanges
object, or from a GFF or GTF file.
The TxDb class.
makeTxDb
for the low-level function used by the
makeTxDbFrom*
functions to make the TxDb object
returned to the user.
txdb <- makeTxDbFromEnsembl("Saccharomyces cerevisiae", server="useastdb.ensembl.org") txdb