read-functions: Import of '.cls' and '.gct' files

In GSRI: Gene Set Regulation Index

Description

Import the groups from ‘.cls’ files and the expression data from ‘.gct’ files.

Usage

readCls(file, ...)
readGct(file, ...)

Arguments

file	Character vector specifying the path of the file to be read in.
...	Optinal arguments, currently not used.

Details

With these methods the expression data and the assignment of the samples to groups can be read from ‘.cls’ (categorical class) and ‘.gct’ (gene cluster text) files, respectively. Details on the specific formats can be found at http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats.

Please note that the readCls method reads only categorical class labels, not continuous ones.

Value

For a ‘.cls’ file, a factor containing the groups.

For a ‘.gct’ file, a matrix containing the expression intensities, with rows corresponding to genes and columns to samples.

Author(s)

Julian Gehring

Maintainer: Julian Gehring <[e-mail]>

See Also

Package: GSRI-package

Class: Gsri

Methods: gsri getGsri getCdf getParms export sortGsri plot show summary readCls readGct

Examples

## Not run: 
exprs <- readGct(file)

groups <- readCls(file)

## End(Not run)

GSRI documentation built on Nov. 8, 2020, 7:46 p.m.