createTxDbFromEnsembl: Creates an EnhancedTxDb object from the ENSEMBL data base.

In jotsetung/EnhancedTxDbs: Storing annotation in TranscriptDb objects

Description

Takes a data base connection to create a EnhancedTxDb based on ENSEMBL. In contrast to the normal TxDb objects EnhancedTxDb objects allow to store also annotation information. At the moment the only used annotation information is the ENSEMBL biotype.

Usage

createTxDbFromEnsembl(version, annotInfo=TRUE,
ensemblApi="/home/bioinfo/ensembl/75/",
bioperl="~/ENSEMBL/bioperl-1.2.3",
species="human", user="anonymous", host="ensembldb.ensembl.org",
pass="", chr=character(), ...)

Arguments

version	Ensembl version from which the object should be created. E.g.: 67
annotInfo	Logical. If TRUE an EnhancedTxDb object is returned. Otherwise a TxDb object is created.
ensemblApi	The path to the Ensembl perl API (if not already in the PERL5LIB environment variable).
bioperl	Location of the BioPerl library.
species	Species for which the TxDb or EnhancedTxDb object should be created. Default is human.
user	Username for the data base. Default is anonuser.
host	Sever where the data base is running.
pass	Password of the chosen data base user. Default no password is set.
chr	Utilized chromosomes. E.g.: chr=c("X", "19")
...	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.