utils: utility functions

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

Description

utility functions

Finds the prefix name

helper fn that handles a number of annoying tasks using saved data

get the name of the package/sqlite file for a FASTA-based annotation NOTE: as of 1.9.25, this is based on DbType.Org.Version

Usage

utils

idStub(x)

getFastaStub(fastaFile)

colAsVector(x, y)

getSupportedAbbreviations(how = c("abbreviation", "reactome"))

getOrganismAbbreviation(organism, how = c("abbreviation", "reactome"))

getOrgDetails(organism)

getTxDbLiteName(fastaFile)

Arguments

x	a string to try and pop the ENSEMBL identifier off of
fastaFile	a FASTA file of interest get the "stub" of a FASTA filename (no .fa, no .fasta, no .gz)
y	a column of a data frame get a column of a data.frame _complete_with_rownames_ as a vector
how	method for finding supported species abbreviations supported organism abbreviations
organism	a familiar organism Get the abbreviation for an organism (among those with which we're familiar)

Format

An object of class NULL of length 0.

Value

if everything works out properly, the ENS* identifier (without .N)

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