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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App Name

MLM Mixed Linear Model (MLM) is a linear model for genome wide association study that reduces false positives by considering complex pedigrees, families, founding effects and population structure.

Quick Start

Test Data

Input File(s)

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Test data can be found in the data window under Community Data -> iplantcollaborative -> example_data -> mlm -> input 

Parameters Used in App

When the app is run in the DE, use the default parameters with the above input files to get the output provided in the next section below.

  • Use the genotype file in HapMap format with extension .hmp.txt as Marker data
  • Other files needed are trait file, population structure file and kinship file.

Output File(s)

Given default output file name mlm, expect mlm1.txt, mlm2.txt and mlm3.txt as output. These files are statistics results of the tests for each trait, estimated effects of each allele for each marker, a table showing the likelihood, genetic variance, and error variance for each compression level tested during the optimization process. 

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1 Comment

  1. ★★★★★ Testing DE. Ignore this. (by narro)