runDecode: Differential Co-Expression and Differential Expression...

Description Usage Arguments Details Examples

View source: R/Decode.r

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

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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

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## 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)

decode documentation built on May 30, 2017, 3 a.m.