read.gct: Read GCT format file which stores the expression values

In jokergoo/CePa: Centrality-Based Pathway Enrichment

Description

Read GCT format file which stores the expression values

Usage

read.gct(file)

Arguments

file	gct file path

Details

The GCT format is a tab delimited file format that stores the expression value matrix. The first line of the file is the version number which always be #1.2. The second line is the number of the size of genes and samples, seperated by space, usually for the initiation of reading the expression matrix. The third line contains a list of identifiers for the samples associated with each of the columns in the remainder of the file. From the fourth line will be the expression value of each gene.

GCT file is used together with CLS file.

Value

A matrix of the expression values, with rows correponding to genes and cols to samples.

Source

https://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats

Author(s)

Zuguang Gu <[e-mail]>

Examples

## Not run: 
# expression data stored in a gct format file
# P53_symbol.gct can be downloaded from
# https://mcube.nju.edu.cn/jwang/lab/soft/cepa/
eset = read.gct("https://mcube.nju.edu.cn/jwang/lab/soft/cepa/P53_symbol.gct")
head(eset)

## End(Not run)

jokergoo/CePa documentation built on July 2, 2021, 10:28 p.m.