ensDbLiteFromFasta: Function to create an EnsDbLite object (a stripped-down...

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

Description

Function to create an EnsDbLite object (a stripped-down SQLite db) from a specified Ensembl FASTA file for a given version, species, and type(s). Note that this is shockingly easier than the same process for the GTF...

Usage

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

getEntrezIDs(gxs, organism)

getSymbols(gxs, organism)

ensDbLiteMetadata(packageName, genomeVersion, sourceFile)

Arguments

fastaFile	the FASTA file to collate into a EnsDbLite instance
verbose	make a lot of noise? (TRUE)
dryRun	boolean if false a sql database is created
gxs	a GRanges of genes
organism	what kind of organism these genes are from
packageName	the name of the annotation package to be built
genomeVersion	name of genome assembly for coordinates, e.g. "GRCh38"
sourceFile	name of FASTA file(s) whence it was built, as a string

Value

entrez_id values for the genes, where found

symbols for the genes, where found

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

Functions

• getEntrezIDs: add EntrezGene IDs for Ensembl genes

• getSymbols: add symbols for Ensembl genes

• ensDbLiteMetadata: create metadata for an EnsDbLite instance

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