The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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MLM Workflow

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Automatic workflow for filtering, numerical conversion, LD, kinship and fitting MLM model.

Quick Start

Test Data


Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> MLM_workflow.

Input File(s)

Use mdp_genotype.hmp.txt and mdp_traits.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.

  • Default parameters only, no further configuration needed.

Output File(s)

Expect multiple text files and one image file as output. For the test case, the output files you will find in the example_data directory are:

  • filterGeno.hmp.txt
  • kinship.txt
  • mlm_filterGeno_+_mdp_traits_compression.txt
  • mlm_filterGeno_+_mdp_traits_effects.txt
  • mlm_filterGeno_+_mdp_traits_stats.txt
  • numGeno.txt
  • output.png

Tool Source for App

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