repDbLiteFromMouseFasta: functions to create a RepDbLite object (a stripped-down...

In arcolombo/TxDbLite: Lightweight SQLite-based annotation classes/packages for use with arkas

Description

functions to create a RepDbLite object (a stripped-down SQLite db) from a specified RepBase FASTA file for a given version, species, and type(s). this is the mouse rep biotype to be used.

Usage

repDbLiteFromMouseFasta(fastaFile, verbose = TRUE, dryRun = FALSE)

repDbLiteMetaMousedata(packageName, sourceFile)

Arguments

fastaFile	the FASTA file to collate into a RepDbLite instance
verbose	make a lot of noise? (TRUE)
dryRun	boolean if false, a sql database is created
packageName	the name of the annotation package to be built
sourceFile	name of FASTA file(s) whence it was built, as a string

Value

a data.frame of metadata suitable for cramming into the database

Functions

• repDbLiteMetaMousedata: create metadata for a RepDbLite instance

arcolombo/TxDbLite documentation built on July 10, 2020, 12:27 a.m.