decode (version 1.2)

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):

Column 1: Official gene symbol

Column 2: Probe ID

Starting from column 3: Expression for different samples

Row 1 (starting from column 3): Sample class ("1" indicates control group; "2" indicates case group)

Row 2: Sample id

Starting from row 3: Expression for different genes

Example:

geneName probeID 2 2 2 1 1 1

- - Case1 Case2 Case3 Control1 Control2 Control3

7A5 ILMN_1762337 5.12621 5.19419 5.06645 5.40649 5.51259 5.387

A1BG ILMN_2055271 5.63504 5.68533 5.66251 5.37466 5.43955 5.50973

A1CF ILMN_2383229 5.41543 5.58543 5.43239 5.49634 5.62685 5.36962

A26C3 ILMN_1653355 5.56713 5.5547 5.59547 5.46895 5.49622 5.50094

A2BP1 ILMN_1814316 5.23016 5.33808 5.31413 5.30586 5.40108 5.31855

A2M ILMN_1745607 7.65332 6.56431 8.20163 9.19837 9.04295 10.1448

A2ML1 ILMN_2136495 5.53532 5.93801 5.33728 5.36676 5.79942 5.13974

A3GALT2 ILMN_1668111 5.18578 5.35207 5.30554 5.26107 5.26536 5.28932

Data format for functional gene set data (Columns are tab-separated):

Column 1: Functional gene set name

Column 2: Other description such as gene set id

Starting from column 3: Official gene symbols for the functional gene set

Example:

B cell activation GO\GO:0042113 AKAP17A ZAP70 PFDN1 ...

apoptotic signaling pathway GO\GO:0097190 ITPR1 PTH DNAJC10 HINT1 ...

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

## Not run: 
# path = system.file('extdata', package='decode')
# geneSetInputFile = file.path(path, "geneSet.txt")
# geneExpressionFile = file.path(path, "Expression_data_50genes.txt")
# runDecode(geneSetInputFile, geneExpressionFile)
# ## End(Not run)