make.gal.env: GAL Environment Maker

In ExiMiR: R functions for the normalization of Exiqon miRNA array data

Description

Reads an Exiqon GAL file and creates an annotation environment used as a hash table for the probeset mapping location.

Usage

make.gal.env(galname=NULL,
             filename=NULL,
             gal.path=getwd(),
             verbose=FALSE)

Arguments

galname	Character vector. Name to be used for the annotation environment.
filename	Character vector. Name of the GAL file.
gal.path	Character vector. Path to the GAL file.
verbose	Logical. The default value is TRUE. The details of the function execution are displayed on the console.

Details

This function is designed similarly to make.cdf.env from the makecdfenv package. If no filename is provided as argument, the function tries to read the first GAL file in the input path. The returned environment is a hash table. For every probeset name we have a matrix with 2 columns. The first column contains the PM locations and the second column the MM locations. For PM only chips the MM column will have NAs.

Value

None.

Author(s)

Sylvain Gubian, Alain Sewer, PMP SA

Examples

# The folder 'Exiqon' contains a GAL file
## Not run: make.gal.env(galname='galenv', gal.path='Exiqon')

ExiMiR documentation built on Nov. 8, 2020, 8:26 p.m.