import.gsea.gct: Import a gct file

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

Description

Import a GenePattern gct file into R as a data.frame object. If a clm.file is also provided, then the columns of the gct are optionally subsetted, reordered, and renamed as per the clm.

Usage

import.gsea.gct(f, clm.file = NULL, check.names = FALSE)

Arguments

f	[character] the path to a gct file
clm.file	[optional] path to a clm.file
check.names	logical: R likes to make sure that the column names are 'syntactically valid', If you don't care, then choose FALSE. default is FALSE.

Value

a data.frame of usually gene expression data. columns 1&2 are annotation, 3+ are data.

Author(s)

Mark Cowley, 2009-07-27

See Also

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

Examples

## Not run: 
f <- "ftp://ftp.broadinstitute.org/pub/genepattern/datasets/all_aml/all_aml_test.gct"
import.gsea.gct(f)

## End(Not run)

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