decode (version 1.1)

runDecode: Differential Co-Expression and Differential Expression Analysis

Description

Given a set of gene expression data and functional gene set data, the program will return a table summary for the selected gene sets with high differential co-expression and high differential expression (HDC-HDE). User need to specify the input paths for the gene expression data and functional gene set data.

Usage

runDecode(geneSetInputFile, geneExpressionFile)

Arguments

geneSetInputFile

Path for functional gene set data

geneExpressionFile

Path for gene expression data Input: (1) gene expression data (2) functional gene set data Output: Table summary for the selected HDC-HDE gene sets, 'out_summary.txt' Data format for gene expression data (Columns are tab-separated):

Details

The main program for DECODE algorithm To run an example using expression data with 1400 genes. runDecode("\extdata\geneSet.txt","\extdata\Expression_data_1400genes.txt") or runDecode("/extdata/geneSet.txt","/extdata/Expression_data_1400genes.txt") The sample data with 1400 genes takes 16 minutes to complete. (Computer used: An Intel Core i7-4600 processor, 2.69 GHz, 8 GB RAM)

Examples

path = system.file('extdata', package='decode')
geneSetInputFile = file.path(path, "geneSet.txt")
geneExpressionFile = file.path(path, "Expression_data_50genes.txt")
runDecode(geneSetInputFile, geneExpressionFile)