export.gsea.gct: Function to export a GenePattern gct file.

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

Description

data can be either:
a matrix or data.frame of numeric values, in which case you can provide an optional description or chip object to populate the “Description” column; or a data.frame containing ‘Name’ and “Description” columns (see import.gsea.gct)

Usage

export.gsea.gct(data, description = NULL, file = NULL, chip = NULL,
  round = 4, version = "#1.2", missing = "", ...)

Arguments

data	a matrix or data.frame WITH rownames of all numeric values, or a data.frame from running import.gsea.gct; ie first 2 columns are “Name”, “Description”.
description	a vector of annotations. IF it has names, then these names must match the rownames of data, in which case we make sure they're in the same order. If no names, then we assume that they're in the same order. If NULL, then you must either provide a chip, or have a “Description” column in the data.
file	the output file name
chip	instead of specifying description, you can specify a GSEA chip object, and a description will be made for you. This overrides description. Default is NULL to ignore.
round	the number of digits to round the numbers to - default=4
version	The GCT file version, to go in the first line.
missing	the string to use for missing data (in the expression data).
...	Currently unused.

Author(s)

Mark Cowley, 2008-08-07

Examples

## Not run: 
my.gct <- import.gsea.gct("./my.gct", "./my.cls")
export.gsea.gct(data=my.gct, file="my2.gct")

## End(Not run)

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