Recent changes to Home

Home modified by liuyang wang

liuyang wang — Wed, 09 Dec 2015 22:38:42 -0000

--- v9
+++ v10
@@ -71,7 +71,7 @@

 # Input files

-An example of user-defined SNP file can be found test/example.txt, which contain 3 columns of chromosome, SNP rsID and p values. The column delimiter is 'tab' not 'space'.
+An example of user-defined SNP file can be found test/example.txt, which contain 3 columns of chromosome, SNP rsID and p values. **The column delimiter is 'tab' **not 'space'.

 Format for the user-defined SNPlist requires 3 columns. However, only the SNP rsIDs is absolutely required for CPAG (column 1 could be filled with "dummy" values and the p-values in column 3 are required only to take advantage of CPAG's p-value filtering options).

Home modified by liuyang wang

liuyang wang — Thu, 24 Sep 2015 13:13:19 -0000

--- v8
+++ v9
@@ -25,7 +25,7 @@

 ## Notes

-*New: The CPAGv0.2 for Mac OS has been updated to provide pleiotropic gene and SNPs lists and was compiled by Python 3.3 (~100 fold improvement in performance over v0.1). Similar improvements are coming soon for Windows.
+***New**: The CPAGv0.2 for Mac OS has been updated to provide pleiotropic gene and SNPs lists and was compiled by Python 3.3 (~100 fold improvement in performance over v0.1). Similar improvements are coming soon for Windows.

 1\.  For windows, you can run CPAG from the windows prompt. You can either 1) double click windows\_prompt.bat in this folder or 2) click Start -> Search "Command Prompt".

Home modified by liuyang wang

liuyang wang — Wed, 20 May 2015 21:41:00 -0000

--- v7
+++ v8
@@ -25,7 +25,7 @@

 ## Notes

-*New: The CPAGv0.2 for Mac OS has been updated to provide pleiotropic gene and SNPs lists and was compiled by Python 3.3 (~100 fold improvement in performance over v0.1). Similar improvements coming soon for Windows.
+*New: The CPAGv0.2 for Mac OS has been updated to provide pleiotropic gene and SNPs lists and was compiled by Python 3.3 (~100 fold improvement in performance over v0.1). Similar improvements are coming soon for Windows.

 1\.  For windows, you can run CPAG from the windows prompt. You can either 1) double click windows\_prompt.bat in this folder or 2) click Start -> Search "Command Prompt".

Home modified by liuyang wang

liuyang wang — Wed, 20 May 2015 21:29:10 -0000

--- v6
+++ v7
@@ -24,6 +24,8 @@
 # Getting started

 ## Notes
+
+*New: The CPAGv0.2 for Mac OS has been updated to provide pleiotropic gene and SNPs lists and was compiled by Python 3.3 (~100 fold improvement in performance over v0.1). Similar improvements coming soon for Windows.

 1\.  For windows, you can run CPAG from the windows prompt. You can either 1) double click windows\_prompt.bat in this folder or 2) click Start -> Search "Command Prompt".

Home modified by liuyang wang

liuyang wang — Wed, 01 Apr 2015 12:58:11 -0000

--- v5
+++ v6
@@ -37,21 +37,21 @@

 ## Quick examples

-1\.  Run usr defined SNPlist against NHGRI GWAS Catalog (Sep4,2013)
+1\.  Run user defined SNPlist against NHGRI GWAS Catalog (Sep4,2013)

-    Note: Usr defined queries will run much faster (likely < 10min) because it computes pairwise similarity just for the usr-definied trait and each trait in the catalog. 
+    Note: User defined queries will run much faster (likely < 10min) because it computes pairwise similarity just for the user-definied trait and each trait in the catalog. 

         CPAG.exe --cpag-diy --diy-gwasfile test/example.txt

-2\.  Run usr defined SNPlist against Autoimmune group of NHGRI GWAS Catalog (Sep4,2013)
+2\.  Run user defined SNPlist against Autoimmune group of NHGRI GWAS Catalog (Sep4,2013)

         CPAG.exe --cpag-diy --diy-gwasfile test/example.txt --disgrp Autoimmune

-3\.  Run usr defined SNPlist against NHGRI GWAS Catalog (Sep4,2013), only including SNPs in the usr-defined SNPlist with p values < 0.00001
+3\.  Run user defined SNPlist against NHGRI GWAS Catalog (Sep4,2013), only including SNPs in the user-defined SNPlist with p values < 0.00001

         CPAG.exe --cpag-diy --diy-gwasfile test/example.txt --diy-gwas-pcut 0.00001

-4\.  Run usr defined SNPlist against Autoimmune group of NHGRI GWAS Catalog (Sep4,2013), only including SNPs in the usr-defined SNPlist with p values < 0.00001
+4\.  Run user defined SNPlist against Autoimmune group of NHGRI GWAS Catalog (Sep4,2013), only including SNPs in the user-defined SNPlist with p values < 0.00001

         CPAG.exe --cpag-diy --diy-gwasfile test/example.txt --diy-gwas-pcut 0.00001 --disgrp Autoimmune

@@ -69,9 +69,9 @@

 # Input files

-An example of usr-defined SNP file can be found test/example.txt, which contain 3 columns of chromosome, SNP rsID and p values. The column delimiter is 'tab' not 'space'.
+An example of user-defined SNP file can be found test/example.txt, which contain 3 columns of chromosome, SNP rsID and p values. The column delimiter is 'tab' not 'space'.

-Format for the usr-defined SNPlist requires 3 columns. However, only the SNP rsIDs is absolutely required for CPAG (column 1 could be filled with "dummy" values and the p-values in column 3 are required only to take advantage of CPAG's p-value filtering options).
+Format for the user-defined SNPlist requires 3 columns. However, only the SNP rsIDs is absolutely required for CPAG (column 1 could be filled with "dummy" values and the p-values in column 3 are required only to take advantage of CPAG's p-value filtering options).

 

@@ -120,21 +120,21 @@

 Output files should be saved in a folder starting with "CPAGresults"

-## Output for usr-defined SNPlist
+## Output for user-defined SNPlist

-1\.  a "mainout" file is a tab-delimited file listing all traits with similarity to the usr-defined trait. For each trait the observed number of overlapping SNPs, the number of overlapping SNPs expected by chance, various p-values, and the Chao-Sorensen similarity index value is provided.
+1\.  a "mainout" file is a tab-delimited file listing all traits with similarity to the user-defined trait. For each trait the observed number of overlapping SNPs, the number of overlapping SNPs expected by chance, various p-values, and the Chao-Sorensen similarity index value is provided.

 2\.  a "ChaoSorensenOneRowHeatmap\_SortByPval" file is a pdf heatmap of color-coded similarity values sorted from low to high pvalue. A red line demarcates the threshold for statistical significance (p<0.05 after Bonferroni correction).

-3\.  a "merge.ChaoSorensen" pdf file that places the usr-defined trait into the NHGRI GWAS Catalog heirarchical tree and heatmap. The usr-defined trait is labeled as Mysnplist\_Mysnplist.
+3\.  a "merge.ChaoSorensen" pdf file that places the user-defined trait into the NHGRI GWAS Catalog heirarchical tree and heatmap. The user-defined trait is labeled as Mysnplist\_Mysnplist.

-4\.  a "mainout\_Network" file is a PNG file with a network showing traits with any similarity to the usr-defined trait and connectivity based on similarity of those traits.
+4\.  a "mainout\_Network" file is a PNG file with a network showing traits with any similarity to the user-defined trait and connectivity based on similarity of those traits.

 5\.  a folder titled "gsea" which contains enrichment of pathways based on overlapping SNPs using the C2 MSigDB (GSEA Broad Institute) and IFN-targets from (Liu et al. 2012).

 ## Output for NHGRI GWAS Catalog

-1\.  a "mainout" file is a tab-delimited file listing all traits with similarity to the usr-defined trait. For each trait the observed number of overlapping SNPs, the number of overlapping SNPs expected by chance, various p-values, and the Chao-Sorensen similarity index value is provided.
+1\.  a "mainout" file is a tab-delimited file listing all traits with similarity to the user-defined trait. For each trait the observed number of overlapping SNPs, the number of overlapping SNPs expected by chance, various p-values, and the Chao-Sorensen similarity index value is provided.

 2\.  a "ChaoSorensen" pdf file that displays then entire NHGRI GWAS Catalog heirarchical tree and heatmap.

Home modified by liuyang wang

liuyang wang — Mon, 06 Oct 2014 20:25:06 -0000

--- v4
+++ v5
@@ -39,7 +39,7 @@

 1\.  Run usr defined SNPlist against NHGRI GWAS Catalog (Sep4,2013)

-    Note: Usr defined queries will run much faster (likely < 10min) because it computes pairwise similarity just for the usr-definied trait and each trait in the catalog. My computer is 
+    Note: Usr defined queries will run much faster (likely < 10min) because it computes pairwise similarity just for the usr-definied trait and each trait in the catalog. 

         CPAG.exe --cpag-diy --diy-gwasfile test/example.txt

Home modified by liuyang wang

liuyang wang — Mon, 06 Oct 2014 20:23:29 -0000

--- v3
+++ v4
@@ -1,72 +1,77 @@
-Welcome to CPAG wiki!
-
 
 Table of Contents
 
 
 1. What's CPAG?
 2. Download CPAG
-3. Get started
+3. Getting started
 4. Input files
 5. Output files
-6. Important notes
 
 
 

-# What's CPAG?
+# What's CPAG?

-CPAG (Cross-Phenotype Analysis of GWAS) can estimate disease and trait similarity, identify informative disease clusters, and carry out pathway enrichment analysis. It also provides visualization of these results in the form of hierarchical clustering trees, heatmaps, and networks.  
+CPAG (Cross-Phenotype Analysis of GWAS) can estimate disease and trait similarity, identify informative disease clusters, and carry out pathway enrichment analysis. It also provides visualization of these
+results in the form of hierarchical clustering trees, heatmaps, and networks.  

-# Download CPAG
+# Download CPAG

-CPAG can be downloaded from [here](https://sourceforge.net/projects/cpag/). Both Windows and Mac version are
-provided, and current version is 0.1.
+CPAG can be downloaded from [here](https://sourceforge.net/projects/cpag/). Both Windows and Mac version are provided, and current version is 0.1.

-# Get started
+# Getting started

-CPAGv0.1\_win.exe or CPAGv0.1\_mac must be placed into same folder with cpaglib
+## Notes

-1\.  Run NHGRI GWAS Catalog only (Sep4,2013), only including SNPs with p values < 0.0000001
+1\.  For windows, you can run CPAG from the windows prompt. You can either 1) double click windows\_prompt.bat in this folder or 2) click Start -> Search "Command Prompt".
+
+2\.  For Mac system, CPAGv0.1\_mac was compiled using Mac OS mavericks 10.9 system.
+
+3\.  CPAG.exe or CPAGv0.1\_mac must be placed into same folder with cpaglib. For Mac, please replace the "CPAG.exe" with "./CPAGv0.1\_mac" in the following examples and run in the Terminal.
+
+4\.  Type "CPAG.exe -h" for help, or check running examples using
+
+        CPAG.exe --show-example
+
+## Quick examples
+
+1\.  Run usr defined SNPlist against NHGRI GWAS Catalog (Sep4,2013)
+
+    Note: Usr defined queries will run much faster (likely < 10min) because it computes pairwise similarity just for the usr-definied trait and each trait in the catalog. My computer is 
+    
+        CPAG.exe --cpag-diy --diy-gwasfile test/example.txt
+
+2\.  Run usr defined SNPlist against Autoimmune group of NHGRI GWAS Catalog (Sep4,2013)
+
+        CPAG.exe --cpag-diy --diy-gwasfile test/example.txt --disgrp Autoimmune
+
+3\.  Run usr defined SNPlist against NHGRI GWAS Catalog (Sep4,2013), only including SNPs in the usr-defined SNPlist with p values < 0.00001
+
+        CPAG.exe --cpag-diy --diy-gwasfile test/example.txt --diy-gwas-pcut 0.00001
+
+4\.  Run usr defined SNPlist against Autoimmune group of NHGRI GWAS Catalog (Sep4,2013), only including SNPs in the usr-defined SNPlist with p values < 0.00001
+
+        CPAG.exe --cpag-diy --diy-gwasfile test/example.txt --diy-gwas-pcut 0.00001 --disgrp Autoimmune
+
+5\.  Plot Network degree
+
+    Note: This function uses the first two columns of a "mainout" file to plot the network along with a distribution of the number of associated traits for each trait within the network.
+    
+        CPAG.exe --plot-network-degree test/example.networkdegree.infile
+
+6\.  Run NHGRI GWAS Catalog only (Sep4,2013), only including SNPs with p values < 0.0000001

         CPAG.exe --cpag-all --cpag-gfile GWASCatalog2013Sep4_p1e-7.txt --cpag-gfile-pcut 0.0000001

-    This may take several hours to run depending on the power of your computer, because it computes all pairwise similarity
+    This may take several hours to run depending on the power of your computer, because it computes all pairwise similarity. The output from running this will be the same as Supplemental Figure 1 and Supplemental Table 2 (Wang et al.), but can be run with different p-value thresholds and newer versions of the NHGRI GWAS Catalog.

-2\.  Run usr defined SNPlist against NHGRI GWAS Catalog (Sep4,2013)
+# Input files

-    Note: Usr defined queries like this will run much faster (likely <10min) because it computes pairwise similarity just for the usr-definied trait and each trait in the catalog
-    
-        CPAG.exe --cpag-diy --diy-gwasfile example.txt
+An example of usr-defined SNP file can be found test/example.txt, which contain 3 columns of chromosome, SNP rsID and p values. The column delimiter is 'tab' not 'space'.

-3\.  Run usr defined SNPlist against Autoimmune group of NHGRI GWAS Catalog (Sep4,2013)
-
-        CPAG.exe --cpag-diy --diy-gwasfile test/example.txt --disgrp Autoimmune
-
-4\.  Run usr defined SNPlist against NHGRI GWAS Catalog (Sep4,2013), only including SNPs in the usr-defined SNPlist with p values < 0.00001
-
-        CPAG.exe --cpag-diy --diy-gwasfile test/example.txt --diy-gwas-pcut 0.00001
-
-5\.  Run usr defined SNPlist against Autoimmune group of NHGRI GWAS Catalog (Sep4,2013), only including SNPs in the usr-defined SNPlist with p values < 0.00001
-
-        CPAG.exe --cpag-diy --diy-gwasfile test/example.txt --diy-gwas-pcut 0.00001 --disgrp Autoimmune
-
-6\.  Plot Network
-
-    Note: only take the prefix of file
-    
-        CPAG.exe --plot-network test/example.network
-
-7\.  Plot Network degree
-
-    Note: Uses the first two columns of the mainout file. This function plots the network along with a distribution of the number of associated traits for each trait within the network.
-    
-        CPAG.exe --plot-network-degree test/example.networkdegree.infile
-
-# Input files
-
-A simple example for usr-defined SNPlist includes 3 columns: chromosome, SNP rsID and p values. The column delimiter is 'tab' not 'space'. 
+Format for the usr-defined SNPlist requires 3 columns. However, only the SNP rsIDs is absolutely required for CPAG (column 1 could be filled with "dummy" values and the p-values in column 3 are required only to take advantage of CPAG's p-value filtering options).

 

@@ -85,7 +90,6 @@
 
-

@@ -94,7 +98,6 @@
 
-

@@ -102,7 +105,6 @@
 
-

@@ -110,53 +112,34 @@
 
-Chr
 rsID
 P  
 
 1
 rs1234
 0.0000001  
 
2
 rs1534
 0.0001  
 
2
 rs2145
 0.0001  
 
 
 

-# Output files
+# Output files

 Output files should be saved in a folder starting with "CPAGresults"

-## Output for usr-defined SNPlist
+## Output for usr-defined SNPlist

 1\.  a "mainout" file is a tab-delimited file listing all traits with similarity to the usr-defined trait. For each trait the observed number of overlapping SNPs, the number of overlapping SNPs expected by chance, various p-values, and the Chao-Sorensen similarity index value is provided.

-2\.  a "ChaoSorensenOneRowHeatmap\_SortByPval" file is a pdf heatmap of color-coded similarity values sorted from low to high pvalue. A red line demarcates the threshold for statistical significance (p<0.05 after Bonferroni correction)
+2\.  a "ChaoSorensenOneRowHeatmap\_SortByPval" file is a pdf heatmap of color-coded similarity values sorted from low to high pvalue. A red line demarcates the threshold for statistical significance (p<0.05 after Bonferroni correction).

-3\.  a "merge.ChaoSorensen" pdf file that places the usr-defined trait into the NHGRI GWAS Catalog heirarchical tree and heatmap
+3\.  a "merge.ChaoSorensen" pdf file that places the usr-defined trait into the NHGRI GWAS Catalog heirarchical tree and heatmap. The usr-defined trait is labeled as Mysnplist\_Mysnplist.

-4\.  a "mainout\_Network" file is a PNG file with a network showing traits with any similarity to the usr-defined trait and connectivity based on similarity of those traits
+4\.  a "mainout\_Network" file is a PNG file with a network showing traits with any similarity to the usr-defined trait and connectivity based on similarity of those traits.

-5\.  a folder titled "gsea" which contains enrichment of pathways based on overlapping SNPs using the C2 MSigDB (GSEA Broad Institute) and IFN-targets from (Liu et al. 2012)
+5\.  a folder titled "gsea" which contains enrichment of pathways based on overlapping SNPs using the C2 MSigDB (GSEA Broad Institute) and IFN-targets from (Liu et al. 2012).

-## Output for NHGRI GWAS Catalog
+## Output for NHGRI GWAS Catalog

 1\.  a "mainout" file is a tab-delimited file listing all traits with similarity to the usr-defined trait. For each trait the observed number of overlapping SNPs, the number of overlapping SNPs expected by chance, various p-values, and the Chao-Sorensen similarity index value is provided.

-2\.  a "ChaoSorensen" pdf file that displays then entire NHGRI GWAS Catalog heirarchical tree and heatmap
+2\.  a "ChaoSorensen" pdf file that displays then entire NHGRI GWAS Catalog heirarchical tree and heatmap.

-3\.  a folder titled "gsea" which contains enrichment of pathways based on overlapping SNPs using the C2 MSigDB (GSEA Broad Institute) and IFN-targets from (Liu et al. 2012)
+3\.  a folder titled "gsea" which contains enrichment of pathways based on overlapping SNPs using the C2 MSigDB (GSEA Broad Institute) and IFN-targets from (Liu et al. 2012).

 This analysis has already been run the Sep4,2013 NHGRI GWAS Catalog and is included.
-Future updates of the software will include automatic updating with the most current version of the NHGRI GWAS Catalog.

-# Important notes
-
-Important notes before running CPAG on Windows or Mac
-
-1\.  For windows, you can run CPAG from the windows prompt. You can either 1) double click windows\_prompt.bat in this folder or 2) click Start -> Search "Command Prompt"
-
-2\.  For Mac system, CPAG should work on 64 bit Mac OS 10.6+
-
-3\.  CPAGv0.1\_win.exe or CPAGv0.1\_mac must be placed into same folder with cpaglib
-
-4\.  Type "CPAG.exe -h" for help, or "CPAG.exe –show-example" for running examples
-
-5\.  An example of usr-defined SNP file can be found test/example.txt, which contain 3 columns of chromosome, SNP rsID and p values. The column delimiter is 'tab' not 'space'.
-
-6\.  Format for the usr-defined SNPlist requires 3 columns. However, only the SNP rsIDs is absolutely required for CPAG (column 1 could be filled with "dummy" values and the p-values in column 3 are required only to take advantage of CPAG's p-value filtering options).
-
-    This analysis has already been run the Sep4,2013 NHGRI GWAS Catalog and is included.
-    Future updates of the software will include automatic updating with the most current version of the NHGRI GWAS Catalog.
+Future updates of the software will include automatic updating with the most current version of the NHGRI GWAS Catalog and the ability to query by gene lists.

Home modified by liuyang wang

liuyang wang — Sun, 05 Oct 2014 03:16:21 -0000

--- v2
+++ v3
@@ -1,6 +1,162 @@
 Welcome to CPAG wiki!

-The wiki uses [Markdown](/p/cpag/wiki/markdown_syntax/) syntax.
+
+Table of Contents
+
+
+1. What's CPAG?
+2. Download CPAG
+3. Get started
+4. Input files
+5. Output files
+6. Important notes
+
+
+

-[[members limit=20]]
-[[download_button]]
+
+# What's CPAG?
+
+CPAG (Cross-Phenotype Analysis of GWAS) can estimate disease and trait similarity, identify informative disease clusters, and carry out pathway enrichment analysis. It also provides visualization of these results in the form of hierarchical clustering trees, heatmaps, and networks.  
+
+# Download CPAG
+
+CPAG can be downloaded from [here](https://sourceforge.net/projects/cpag/). Both Windows and Mac version are
+provided, and current version is 0.1.
+
+# Get started
+
+CPAGv0.1\_win.exe or CPAGv0.1\_mac must be placed into same folder with cpaglib
+
+1\.  Run NHGRI GWAS Catalog only (Sep4,2013), only including SNPs with p values < 0.0000001
+
+        CPAG.exe --cpag-all --cpag-gfile GWASCatalog2013Sep4_p1e-7.txt --cpag-gfile-pcut 0.0000001
+    
+    This may take several hours to run depending on the power of your computer, because it computes all pairwise similarity
+
+2\.  Run usr defined SNPlist against NHGRI GWAS Catalog (Sep4,2013)
+
+    Note: Usr defined queries like this will run much faster (likely <10min) because it computes pairwise similarity just for the usr-definied trait and each trait in the catalog
+    
+        CPAG.exe --cpag-diy --diy-gwasfile example.txt
+
+3\.  Run usr defined SNPlist against Autoimmune group of NHGRI GWAS Catalog (Sep4,2013)
+
+        CPAG.exe --cpag-diy --diy-gwasfile test/example.txt --disgrp Autoimmune
+
+4\.  Run usr defined SNPlist against NHGRI GWAS Catalog (Sep4,2013), only including SNPs in the usr-defined SNPlist with p values < 0.00001
+
+        CPAG.exe --cpag-diy --diy-gwasfile test/example.txt --diy-gwas-pcut 0.00001
+
+5\.  Run usr defined SNPlist against Autoimmune group of NHGRI GWAS Catalog (Sep4,2013), only including SNPs in the usr-defined SNPlist with p values < 0.00001
+
+        CPAG.exe --cpag-diy --diy-gwasfile test/example.txt --diy-gwas-pcut 0.00001 --disgrp Autoimmune
+
+6\.  Plot Network
+
+    Note: only take the prefix of file
+    
+        CPAG.exe --plot-network test/example.network
+
+7\.  Plot Network degree
+
+    Note: Uses the first two columns of the mainout file. This function plots the network along with a distribution of the number of associated traits for each trait within the network.
+    
+        CPAG.exe --plot-network-degree test/example.networkdegree.infile
+
+# Input files
+
+A simple example for usr-defined SNPlist includes 3 columns: chromosome, SNP rsID and p values. The column delimiter is 'tab' not 'space'. 
+
+
+
+
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++
+
+
+
+
+
+
+
+
+
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+
+
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+




Chr rsID P  
1 rs1234 0.0000001  
2 rs1534 0.0001  
2 rs2145 0.0001  
+
+# Output files
+
+Output files should be saved in a folder starting with "CPAGresults"
+
+## Output for usr-defined SNPlist
+
+1\.  a "mainout" file is a tab-delimited file listing all traits with similarity to the usr-defined trait. For each trait the observed number of overlapping SNPs, the number of overlapping SNPs expected by chance, various p-values, and the Chao-Sorensen similarity index value is provided.
+
+2\.  a "ChaoSorensenOneRowHeatmap\_SortByPval" file is a pdf heatmap of color-coded similarity values sorted from low to high pvalue. A red line demarcates the threshold for statistical significance (p<0.05 after Bonferroni correction)
+
+3\.  a "merge.ChaoSorensen" pdf file that places the usr-defined trait into the NHGRI GWAS Catalog heirarchical tree and heatmap
+
+4\.  a "mainout\_Network" file is a PNG file with a network showing traits with any similarity to the usr-defined trait and connectivity based on similarity of those traits
+
+5\.  a folder titled "gsea" which contains enrichment of pathways based on overlapping SNPs using the C2 MSigDB (GSEA Broad Institute) and IFN-targets from (Liu et al. 2012)
+
+## Output for NHGRI GWAS Catalog
+
+1\.  a "mainout" file is a tab-delimited file listing all traits with similarity to the usr-defined trait. For each trait the observed number of overlapping SNPs, the number of overlapping SNPs expected by chance, various p-values, and the Chao-Sorensen similarity index value is provided.
+
+2\.  a "ChaoSorensen" pdf file that displays then entire NHGRI GWAS Catalog heirarchical tree and heatmap
+
+3\.  a folder titled "gsea" which contains enrichment of pathways based on overlapping SNPs using the C2 MSigDB (GSEA Broad Institute) and IFN-targets from (Liu et al. 2012)
+
+This analysis has already been run the Sep4,2013 NHGRI GWAS Catalog and is included.
+Future updates of the software will include automatic updating with the most current version of the NHGRI GWAS Catalog.
+
+# Important notes
+
+Important notes before running CPAG on Windows or Mac
+
+1\.  For windows, you can run CPAG from the windows prompt. You can either 1) double click windows\_prompt.bat in this folder or 2) click Start -> Search "Command Prompt"
+
+2\.  For Mac system, CPAG should work on 64 bit Mac OS 10.6+
+
+3\.  CPAGv0.1\_win.exe or CPAGv0.1\_mac must be placed into same folder with cpaglib
+
+4\.  Type "CPAG.exe -h" for help, or "CPAG.exe –show-example" for running examples
+
+5\.  An example of usr-defined SNP file can be found test/example.txt, which contain 3 columns of chromosome, SNP rsID and p values. The column delimiter is 'tab' not 'space'.
+
+6\.  Format for the usr-defined SNPlist requires 3 columns. However, only the SNP rsIDs is absolutely required for CPAG (column 1 could be filled with "dummy" values and the p-values in column 3 are required only to take advantage of CPAG's p-value filtering options).
+
+    This analysis has already been run the Sep4,2013 NHGRI GWAS Catalog and is included.
+    Future updates of the software will include automatic updating with the most current version of the NHGRI GWAS Catalog.

Home modified by liuyang wang

liuyang wang — Sun, 05 Oct 2014 03:15:35 -0000

--- v1
+++ v2
@@ -1,6 +1,4 @@
-Welcome to your wiki!
-
-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
+Welcome to CPAG wiki!

 The wiki uses [Markdown](/p/cpag/wiki/markdown_syntax/) syntax.

Discussion for Home page

liuyang wang — Sun, 05 Oct 2014 03:11:29 -0000

1. What's CPAG?
2. Download CPAG
3. Get started
4. Input files
5. Output files
6. Important notes

What's CPAG?

CPAG (Cross-Phenotype Analysis of GWAS) can estimate disease and trait
similarity, identify informative disease clusters, and carry out
pathway enrichment analysis. It also provides visualization of these
results in the form of hierarchical clustering trees, heatmaps, and networks.

Download CPAG

CPAG can be downloaded from here. Both Windows and Mac version are
provided, and current version is 0.1.

Get started

CPAGv0.1_win.exe or CPAGv0.1_mac must be placed into same folder with cpaglib

1. Run NHGRI GWAS Catalog only (Sep4,2013), only including SNPs with p values < 0.0000001

    CPAG.exe --cpag-all --cpag-gfile GWASCatalog2013Sep4_p1e-7.txt --cpag-gfile-pcut 0.0000001

This may take several hours to run depending on the power of your computer, because it computes all pairwise similarity

2. Run usr defined SNPlist against NHGRI GWAS Catalog (Sep4,2013)

Note: Usr defined queries like this will run much faster (likely <10min) because it computes pairwise similarity just for the usr-definied trait and each trait in the catalog

    CPAG.exe --cpag-diy --diy-gwasfile example.txt

3. Run usr defined SNPlist against Autoimmune group of NHGRI GWAS Catalog (Sep4,2013)

    CPAG.exe --cpag-diy --diy-gwasfile test/example.txt --disgrp Autoimmune

4. Run usr defined SNPlist against NHGRI GWAS Catalog (Sep4,2013), only including SNPs in the usr-defined SNPlist with p values < 0.00001

    CPAG.exe --cpag-diy --diy-gwasfile test/example.txt --diy-gwas-pcut 0.00001

5. Run usr defined SNPlist against Autoimmune group of NHGRI GWAS Catalog (Sep4,2013), only including SNPs in the usr-defined SNPlist with p values < 0.00001

    CPAG.exe --cpag-diy --diy-gwasfile test/example.txt --diy-gwas-pcut 0.00001 --disgrp Autoimmune

6. Plot Network

Note: only take the prefix of file

    CPAG.exe --plot-network test/example.network

7. Plot Network degree

Note: Uses the first two columns of the mainout file. This function plots the network along with a distribution of the number of associated traits for each trait within the network.

    CPAG.exe --plot-network-degree test/example.networkdegree.infile

Input files

A simple example for usr-defined SNPlist includes 3 columns: chromosome, SNP rsID and p values. The column delimiter is 'tab' not 'space'.

Chr	rsID	P
1	rs1234	0.0000001
2	rs1534	0.0001
2	rs2145	0.0001

Output files

Output files should be saved in a folder starting with "CPAGresults"

Output for usr-defined SNPlist

1. a "mainout" file is a tab-delimited file listing all traits with similarity to the usr-defined trait. For each trait the observed number of overlapping SNPs, the number of overlapping SNPs expected by chance, various p-values, and the Chao-Sorensen similarity index value is provided.
2. a "ChaoSorensenOneRowHeatmap_SortByPval" file is a pdf heatmap of color-coded similarity values sorted from low to high pvalue. A red line demarcates the threshold for statistical significance (p<0.05 after Bonferroni correction)
3. a "merge.ChaoSorensen" pdf file that places the usr-defined trait into the NHGRI GWAS Catalog heirarchical tree and heatmap
4. a "mainout_Network" file is a PNG file with a network showing traits with any similarity to the usr-defined trait and connectivity based on similarity of those traits
5. a folder titled "gsea" which contains enrichment of pathways based on overlapping SNPs using the C2 MSigDB (GSEA Broad Institute) and IFN-targets from (Liu et al. 2012)

Output for NHGRI GWAS Catalog

This analysis has already been run the Sep4,2013 NHGRI GWAS Catalog and is included.
Future updates of the software will include automatic updating with the most current version of the NHGRI GWAS Catalog.

Important notes

Important notes before running CPAG on Windows or Mac

1. For windows, you can run CPAG from the windows prompt. You can either 1) double click windows_prompt.bat in this folder or 2) click Start -> Search "Command Prompt"

2. For Mac system, CPAG should work on 64 bit Mac OS 10.6+

3. CPAGv0.1_win.exe or CPAGv0.1_mac must be placed into same folder with cpaglib

4. Type "CPAG.exe -h" for help, or "CPAG.exe –show-example" for running examples

5. An example of usr-defined SNP file can be found test/example.txt, which contain 3 columns of chromosome, SNP rsID and p values. The column delimiter is 'tab' not 'space'.

6. Format for the usr-defined SNPlist requires 3 columns. However, only the SNP rsIDs is absolutely required for CPAG (column 1 could be filled with "dummy" values and the p-values in column 3 are required only to take advantage of CPAG's p-value filtering options).

This analysis has already been run the Sep4,2013 NHGRI GWAS Catalog and is included.
Future updates of the software will include automatic updating with the most current version of the NHGRI GWAS Catalog.