import.gsea.cls: Import a cls file

In drmjc/metaGSEA: Meta-analysis of GSEA analyses, including intra- and inter-experiment comparisons

Description

Import a GenePattern cls file into R. CLS files can either be categorical, or continuous & both can be handled by this code.

Usage

import.gsea.cls(file, as.factor = TRUE, enforce.zero.start = TRUE)

Arguments

file	the path to a valid cls file.
as.factor	logical: return a character, or factor?
enforce.zero.start	logical: check that the lowest class is 0. See details.

Details

The cls file spec says for catgegorical cls files, values should start from 0. However some tools (eg SubMap) require them to start from 1. enforce.zero.start allows control over these situations.

Value

if cls file is continuous, either a character vector, or factor, one element per sample, of if continuous, a numeric is returned.

Author(s)

Mark Cowley, 2009-11-26

See Also

import.gsea.gct import.gsea.clm http://www.broadinstitute.org/cancer/software/genepattern/tutorial/gp_fileformats.html#cls

drmjc/metaGSEA documentation built on Aug. 8, 2020, 1:53 p.m.