GetTxDb: Download a new or load an existing reference transcriptome.

In mevers/RNAModR: Functional Analysis of RNA Modifications

Description

Download a new or load an existing reference transcriptome. See 'Details'.

Usage

GetTxDb(genomeVersion = "hg38", standardChrOnly = TRUE,
  force = FALSE, verbose = FALSE)

Arguments

genomeVersion	A character string; refers to a specific reference genome assembly version; default is "hg38".
standardChrOnly	A logical scalar; if TRUE and a new db is created, keep only fully assembled chromosomes; default is TRUE.
force	A logical scalar; if TRUE force download and overwrite existing db file; default is FALSE.
verbose	A logical scalar; print additional information about db; default is FALSE.

Details

This is a low-level function that is being called from BuildTx. If no local transcriptome db file exists or forceDownload is TRUE, the function generates an reference transcriptome by calling makeTxDbFromUCSC from the GenomicFeatures package; the return object is a TxDb object and is saved locally as an sqlite db. Details on the txdb return object can be obtained from print(x), where x is the name of the txdb return object. The user may generate a custom transcriptome (e.g. based on a different gene annotation) using makeTxDb or makeTxDb-derived functions from the GenomicFeatures package. Please see the GenomicFeatures reference manual. In order to use a custom transcriptome, the TxDb object needs to be saved locally as an sqlite db, e.g. saveDb(x), "txdb_y.sqlite"), where x is the TxDb object and y denotes the reference genome version as in genomeVersion.

Value

A TxDb object. See 'Details'.

Author(s)

Maurits Evers, [e-mail]

Examples

## Not run: 
txdb <- GetTxDb();
print(txdb);

## End(Not run)

mevers/RNAModR documentation built on Nov. 17, 2019, 9:11 a.m.