runDecode: Differential Co-Expression and Differential Expression...
In decode: Differential Co-Expression and Differential Expression Analysis
Description
Usage
Arguments
Details
Examples
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
1
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
1
2
3
4
5
6
7
## 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)
Example output
[1] "Reading gene expression data..."
[1] "Calculating t-statistics..."
[1] "Calculating pairwise correlation for normal states..."
[1] "Calculating pairwise correlation for disease states..."
[1] "Calculating differential co-expression measures ..."
[1] "Reading functional gene set data"
[1] "Identifying optimal thresholds for genes"
[1] "Gene id: 1"
[1] "Gene id: 2"
[1] "Gene id: 3"
[1] "Gene id: 4"
[1] "Gene id: 5"
[1] "Gene id: 6"
[1] "Gene id: 7"
[1] "Gene id: 8"
[1] "Gene id: 9"
[1] "Gene id: 10"
[1] "Gene id: 11"
[1] "Gene id: 12"
[1] "Gene id: 13"
[1] "Gene id: 14"
[1] "Gene id: 15"
[1] "Gene id: 16"
[1] "Gene id: 17"
[1] "Gene id: 18"
[1] "Gene id: 19"
[1] "Gene id: 20"
[1] "Gene id: 21"
[1] "Gene id: 22"
[1] "Gene id: 23"
[1] "Gene id: 24"
[1] "Gene id: 25"
[1] "Gene id: 26"
[1] "Gene id: 27"
[1] "Gene id: 28"
[1] "Gene id: 29"
[1] "Gene id: 30"
[1] "Gene id: 31"
[1] "Gene id: 32"
[1] "Gene id: 33"
[1] "Gene id: 34"
[1] "Gene id: 35"
[1] "Gene id: 36"
[1] "Gene id: 37"
[1] "Gene id: 38"
[1] "Gene id: 39"
[1] "Gene id: 40"
[1] "Gene id: 41"
[1] "Gene id: 42"
[1] "Gene id: 43"
[1] "Gene id: 44"
[1] "Gene id: 45"
[1] "Gene id: 46"
[1] "Gene id: 47"
[1] "Gene id: 48"
[1] "Gene id: 49"
[1] "Gene id: 50"
[1] "Identifying best associated functional gene set for each gene..."
[1] "Gene id: 1"
[1] "Gene id: 2"
[1] "Gene id: 3"
[1] "Gene id: 4"
[1] "Gene id: 5"
[1] "Gene id: 6"
[1] "Gene id: 7"
[1] "Gene id: 8"
[1] "Gene id: 9"
[1] "Gene id: 10"
[1] "Gene id: 11"
[1] "Gene id: 12"
[1] "Gene id: 13"
[1] "Gene id: 14"
[1] "Gene id: 15"
[1] "Gene id: 16"
[1] "Gene id: 17"
[1] "Gene id: 18"
[1] "Gene id: 19"
[1] "Gene id: 20"
[1] "Gene id: 21"
[1] "Gene id: 22"
[1] "Gene id: 23"
[1] "Gene id: 24"
[1] "Gene id: 25"
[1] "Gene id: 26"
[1] "Gene id: 27"
[1] "Gene id: 28"
[1] "Gene id: 29"
[1] "Gene id: 30"
[1] "Gene id: 31"
[1] "Gene id: 32"
[1] "Gene id: 33"
[1] "Gene id: 34"
[1] "Gene id: 35"
[1] "Gene id: 36"
[1] "Gene id: 37"
[1] "Gene id: 38"
[1] "Gene id: 39"
[1] "Gene id: 40"
[1] "Gene id: 41"
[1] "Gene id: 42"
[1] "Gene id: 43"
[1] "Gene id: 44"
[1] "Gene id: 45"
[1] "Gene id: 46"
[1] "Gene id: 47"
[1] "Gene id: 48"
[1] "Gene id: 49"
[1] "Gene id: 50"
[1] "Processing raw results..."
[1] "Summarizing functional gene set results..."
[1] "Done. Result is saved in out_summary.txt"
Warning message:
In strsplit(oneLine, "\t") : input string 1 is invalid in this locale
decode documentation built on May 2, 2019, 11:28 a.m.
R Package Documentation
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Description Usage Arguments Details Examples
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
1 | 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
1 2 3 4 5 6 7 | ## 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)
|
Example output
[1] "Reading gene expression data..."
[1] "Calculating t-statistics..."
[1] "Calculating pairwise correlation for normal states..."
[1] "Calculating pairwise correlation for disease states..."
[1] "Calculating differential co-expression measures ..."
[1] "Reading functional gene set data"
[1] "Identifying optimal thresholds for genes"
[1] "Gene id: 1"
[1] "Gene id: 2"
[1] "Gene id: 3"
[1] "Gene id: 4"
[1] "Gene id: 5"
[1] "Gene id: 6"
[1] "Gene id: 7"
[1] "Gene id: 8"
[1] "Gene id: 9"
[1] "Gene id: 10"
[1] "Gene id: 11"
[1] "Gene id: 12"
[1] "Gene id: 13"
[1] "Gene id: 14"
[1] "Gene id: 15"
[1] "Gene id: 16"
[1] "Gene id: 17"
[1] "Gene id: 18"
[1] "Gene id: 19"
[1] "Gene id: 20"
[1] "Gene id: 21"
[1] "Gene id: 22"
[1] "Gene id: 23"
[1] "Gene id: 24"
[1] "Gene id: 25"
[1] "Gene id: 26"
[1] "Gene id: 27"
[1] "Gene id: 28"
[1] "Gene id: 29"
[1] "Gene id: 30"
[1] "Gene id: 31"
[1] "Gene id: 32"
[1] "Gene id: 33"
[1] "Gene id: 34"
[1] "Gene id: 35"
[1] "Gene id: 36"
[1] "Gene id: 37"
[1] "Gene id: 38"
[1] "Gene id: 39"
[1] "Gene id: 40"
[1] "Gene id: 41"
[1] "Gene id: 42"
[1] "Gene id: 43"
[1] "Gene id: 44"
[1] "Gene id: 45"
[1] "Gene id: 46"
[1] "Gene id: 47"
[1] "Gene id: 48"
[1] "Gene id: 49"
[1] "Gene id: 50"
[1] "Identifying best associated functional gene set for each gene..."
[1] "Gene id: 1"
[1] "Gene id: 2"
[1] "Gene id: 3"
[1] "Gene id: 4"
[1] "Gene id: 5"
[1] "Gene id: 6"
[1] "Gene id: 7"
[1] "Gene id: 8"
[1] "Gene id: 9"
[1] "Gene id: 10"
[1] "Gene id: 11"
[1] "Gene id: 12"
[1] "Gene id: 13"
[1] "Gene id: 14"
[1] "Gene id: 15"
[1] "Gene id: 16"
[1] "Gene id: 17"
[1] "Gene id: 18"
[1] "Gene id: 19"
[1] "Gene id: 20"
[1] "Gene id: 21"
[1] "Gene id: 22"
[1] "Gene id: 23"
[1] "Gene id: 24"
[1] "Gene id: 25"
[1] "Gene id: 26"
[1] "Gene id: 27"
[1] "Gene id: 28"
[1] "Gene id: 29"
[1] "Gene id: 30"
[1] "Gene id: 31"
[1] "Gene id: 32"
[1] "Gene id: 33"
[1] "Gene id: 34"
[1] "Gene id: 35"
[1] "Gene id: 36"
[1] "Gene id: 37"
[1] "Gene id: 38"
[1] "Gene id: 39"
[1] "Gene id: 40"
[1] "Gene id: 41"
[1] "Gene id: 42"
[1] "Gene id: 43"
[1] "Gene id: 44"
[1] "Gene id: 45"
[1] "Gene id: 46"
[1] "Gene id: 47"
[1] "Gene id: 48"
[1] "Gene id: 49"
[1] "Gene id: 50"
[1] "Processing raw results..."
[1] "Summarizing functional gene set results..."
[1] "Done. Result is saved in out_summary.txt"
Warning message:
In strsplit(oneLine, "\t") : input string 1 is invalid in this locale
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