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jschust authored Jul 1, 2020
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Expand Up @@ -92,31 +92,31 @@ To view the summary information for a particular cluster or sample, enter "info

## 1. Getting Started

• Create the Gene Set File 1. This must be a text file with one line per sample. Each line has the format <Sample Identifier> = <HGNC Symbol 1>, <HGNC Symbol 2>, ..., <HGNC Symbol n> for a sample with n seed genes.
* Create the Gene Set File 1. This must be a text file with one line per sample. Each line has the format <Sample Identifier> = <HGNC Symbol 1>, <HGNC Symbol 2>, ..., <HGNC Symbol n> for a sample with n seed genes.

• (Optional) If you wish to analyze a dichotomous phenotype, a second gene set file can be created for Gene Set 2. This file must be formatted the same way as done for Gene Set 1.
* (Optional) If you wish to analyze a dichotomous phenotype, a second gene set file can be created for Gene Set 2. This file must be formatted the same way as done for Gene Set 1.

## 2. Running Proteinarium

* *Selecting Files*
*Selecting Files*

• In the GUI, select **File > New analysis**
* In the GUI, select **File > New analysis**

• Choose the data files for upload. If you are only analyzing one group or a single sample, leave the Geneset File 2 file field empty. NOTE: If you would like to select new Gene Set Files, click on the “Clear Gene Files” button before selecting new Gene Set Files.
* Choose the data files for upload. If you are only analyzing one group or a single sample, leave the Geneset File 2 file field empty. NOTE: If you would like to select new Gene Set Files, click on the “Clear Gene Files” button before selecting new Gene Set Files.

• Enter a Project Name into the field “Project Name”. If left blank, the program default to the project name “SIM”
* Enter a Project Name into the field “Project Name”. If left blank, the program default to the project name “SIM”

* *Setting Parameters – Configuration File*
• Before running Proteinarium, confirm or make changes to the program’s configurable parameters. A table with all possible parameters, their definitions and their default settings are provided by selecting Help > Available Configurations.
*Setting Parameters – Configuration File*
* Before running Proteinarium, confirm or make changes to the program’s configurable parameters. A table with all possible parameters, their definitions and their default settings are provided by selecting Help > Available Configurations.

• Select File > Settings or “Settings” button to view and change parameters. If any changes are made click “Apply Changes” before exiting. NOTE: The values of the parameters for a New Analysis are not all set to the Default values. These are the values used in our testing and validation with bootstrapping turned off (ie 0 iterations).
* Select **File > Settings** or “Settings” button to view and change parameters. If any changes are made click “Apply Changes” before exiting. NOTE: The values of the parameters for a New Analysis are not all set to the Default values. These are the values used in our testing and validation with bootstrapping turned off (ie 0 iterations).

• For Advance Settings Select File > Settings and click on the “Advance Settings” button. Once changed click on “Set Settings” and the “Apply Changes” buttons.
* For Advance Settings Select File > Settings and click on the “Advance Settings” button. Once changed click on “Set Settings” and the “Apply Changes” buttons.

* *Running Proteinarium*
• Once files are uploaded and parameters are set, click “Run Proteinarium”
*Running Proteinarium*
* Once files are uploaded and parameters are set, click “Run Proteinarium”

• If more than one sample is contained within the input file (s), the dendrogam will be displayed. All output files generated by Proteinarium will be saved to the folder specified by the outputDirectory configuration option. By default, this goes to a folder called “Output” in the same directory as the Proteinarium.jar file.
* If more than one sample is contained within the input file (s), the dendrogam will be displayed. All output files generated by Proteinarium will be saved to the folder specified by the outputDirectory configuration option. By default, this goes to a folder called “Output” in the same directory as the Proteinarium.jar file.

o **<projectName>_ClusterAnalyses.csv:** cluster analysis files

Expand All @@ -127,13 +127,13 @@ To view the summary information for a particular cluster or sample, enter "info

## 3. Viewing Clusters

• When Proteinarium is done running, the GUI will navigate to a new window in which you can input the Cluster/Sample ID for which you are interesting in viewing or obtaining more information.
* When Proteinarium is done running, the GUI will navigate to a new window in which you can input the Cluster/Sample ID for which you are interesting in viewing or obtaining more information.

• Enter sample ID or branch number (ex: C12) in the space provided.
* Enter sample ID or branch number (ex: C12) in the space provided.

• Select either “View Cluster” or “Get Cluster Information”.
* Select either “View Cluster” or “Get Cluster Information”.

• If “View Cluster” is selected, the corresponding the output files will be available in the \<outputDirectory\>/<cluster or sample ID\> folder. And the following files are generated:
* If “View Cluster” is selected, the corresponding the output files will be available in the \<outputDirectory\>/<cluster or sample ID\> folder. And the following files are generated:
o **<cluster or sample ID>_Dendrogram.txt**

o For each of the five possible output networks--Group 1, Group 2, [Group 1 + Group 2], [Group 1 - Group 2], [Group 2 - Group 1], three files are generated to summarize that network. For example:
Expand All @@ -144,7 +144,7 @@ To view the summary information for a particular cluster or sample, enter "info

3. **<cluster or sample ID>_Group1.png:** image of the network

• If “Get Cluster Information” is selected, the following information will be appended to the file “SystemsOutput.txt” as indicated by the text box of the GUI.
* If “Get Cluster Information” is selected, the following information will be appended to the file “SystemsOutput.txt” as indicated by the text box of the GUI.
* *Average Distance (Height)*
* *Bootstrapping Confidence*
* *Total Number of Samples*
Expand All @@ -159,20 +159,20 @@ To view the summary information for a particular cluster or sample, enter "info
* *Group 1 Patients* (Sample IDs of the individuals)
* *Group 2 Patients* (Sample IDs of the individuals)

• Output files can be opened from the GUI: select File > Open to open a file explorer window.
* Output files can be opened from the GUI: select File > Open to open a file explorer window.


## 4. Change the Parameter Configuration and Re-run Proteinarium:

• Select File > Home to return to main screen for running Proteinarium
* Select **File > Home** to return to main screen for running Proteinarium

• Select File > Settings
* Select **File > Settings**

• Change desired parameter values
* Change desired parameter values

• Click Apply Changes
* Click Apply Changes

• Click “Run Proteinarium” to re-run Proteinarium with new configuration. NOTE: Change Project Name otherwise the previous data will be overwritten.
* Click “Run Proteinarium” to re-run Proteinarium with new configuration. NOTE: Change Project Name otherwise the previous data will be overwritten.



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