runDecode function

Differential Co-Expression and Differential Expression Analysis

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.

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)