readAnnotationFile {clValid}

Read in biological annotation files from external file

Description

This function reads in a biological annotation file detailing the functional classes for a given set of genes from a comma separated file.

Usage

readAnnotationFile(filename)

Arguments

filename

The name of the external file. The values must be comma separated.

Details

The required format is comma separated, with the first column indicating the biological functional category, and the remaining columns containing the gene identifiers for those genes belonging to that category.

Value

Returns a list where each item in the list is the set of genes belonging to a particular functional class. This can be converted to a TRUE/FALSE matrix using the annotationListToMatrix function, though it is not necessary to do this prior to using clValid.

Author(s)

Guy Brock, Vasyl Pihur

See Also

annotationListToMatrix, clValid

Examples

## For example use, see the package vignette