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Plots genetic base-pairs sorted by chromosome on the x-axis and negative log of p-values on the y-axis (aka., a Manhattan plot) using ggplot2 from the results file of a FaST-LMM GWAS analysis.
Quick
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StartÂ
- To use FaST-LMM Results Plotter 2, have your FaST-LMM output file somewhere in your data store!
- Open the application through the DE interface.
- Select a title for your analysis.
- Click the second section to select the FaST-LMM output file as your new input.
- Click "Launch Analysis"!
Test Data
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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> directory. |
Input File(s)
Use TerriblyIncomprehensible.txt and HorriblyWritten.txt from the directory above as test input.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
Use either the "Default parameters..." section OR fill in the "Use these parameters..." section. Delete the unused section and the OR. Then, delete this note.
- Default parameters only, no further configuration needed.
OR
- Use these parameters within the DE app interface:
- parameter name - value/setting
- parameter name - value/setting
Output File(s)
Expect a text file named after the input files as output. For the test case, the output file you will find in the example_data directory is named BeautifulProse.txt.