getChrominfo: Retrieves chromosome lenght information from the Ensembl...

In jotsetung/EnhancedTxDbs: Storing annotation in TranscriptDb objects

Description

This function uses a perl script to retrieve the chromosome length information from an Ensembl database (using the Ensembl perl API).

Usage

getChrominfo(version, ensemblApi, species, user="anonymous", host="ensembldb.ensembl.org", pass="", outfile, ... )

Arguments

version	Ensembl version from which the object should be created. E.g.: 67
ensemblApi	The path to the Ensembl perl API (if not already in the PERL5LIB environment variable).
species	Species. Default is human.
user	Username for the data base. Default is anonymous.
host	Sever where the data base is running.
pass	Password of the chosen data base user. Default no password is set.
outfile	The file name of the output file that is generated by the perl script. Defaults to: chrominfo-Ensembl-<version>-<species>.txt
...	Arguments to be passed to or from methods.

Details

Making a TxDb or a EnhancedTxDb object from ENSEMBL containing annotation information from ENSEMBL. The function utilizes a perl script to retrieve the required information from ENSEMBL. To make the function work it is essential to have the ENSEMBL Perl API installed on your machine and that the provided data base connection is correct.

Value

Returns either a EnhancedTxDb object containing the coordinates and annotation of the provided ENSEMBL version or a TxDb providing only the genomic coordinates of the transcripts, exons, cds and genes.

Author(s)

D. Bindreither

See Also

TxDb, GRangesList

Examples

## Not run: 
  ## TranscriptDb-object
  txdb <- createTxDbFromEnsembl(75, annotInfo=FALSE, chr=19)
  txdb

  ## EnhancedTxDb-object
  etxdb <- createTxDbFromEnsembl(75, chr=19)
  etxdb

## End(Not run)

jotsetung/EnhancedTxDbs documentation built on May 19, 2019, 9:41 p.m.