Mercurial > repos > miller-lab > genome_diversity
comparison evaluate_population_numbers.xml @ 17:a3af29edcce2
Uploaded Miller Lab Devshed version a51c894f5bed
| author | miller-lab |
|---|---|
| date | Fri, 28 Sep 2012 11:57:18 -0400 |
| parents | 8ae67e9fb6ff |
| children |
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| 16:be0e2223c531 | 17:a3af29edcce2 |
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| 1 <tool id="gd_evaluate_population_numbers" name="Population Complexity" version="1.0.0"> | |
| 2 <description>: Evaluate possible numbers of ancestral populations</description> | |
| 3 | |
| 4 <command interpreter="bash"> | |
| 5 evaluate_population_numbers.bash "${input.extra_files_path}/admix.ped" "$output" "$max_populations" | |
| 6 </command> | |
| 7 | |
| 8 <inputs> | |
| 9 <param name="input" type="data" format="gd_ped" label="Dataset" /> | |
| 10 <param name="max_populations" type="integer" min="1" value="5" label="Maximum number of populations" /> | |
| 11 </inputs> | |
| 12 | |
| 13 <outputs> | |
| 14 <data name="output" format="txt" /> | |
| 15 </outputs> | |
| 16 | |
| 17 <!-- | |
| 18 <tests> | |
| 19 <test> | |
| 20 <param name="input" value="fake" ftype="gd_ped" > | |
| 21 <metadata name="base_name" value="admix" /> | |
| 22 <composite_data value="test_out/prepare_population_structure/prepare_population_structure.html" /> | |
| 23 <composite_data value="test_out/prepare_population_structure/admix.ped" /> | |
| 24 <composite_data value="test_out/prepare_population_structure/admix.map" /> | |
| 25 <edit_attributes type="name" value="fake" /> | |
| 26 </param> | |
| 27 <param name="max_populations" value="2" /> | |
| 28 | |
| 29 <output name="output" file="test_out/evaluate_population_numbers/evaluate_population_numbers.txt" /> | |
| 30 </test> | |
| 31 </tests> | |
| 32 --> | |
| 33 | |
| 34 <help> | |
| 35 | |
| 36 **Dataset formats** | |
| 37 | |
| 38 The input dataset is in gd_ped_ format. | |
| 39 The output dataset is text. (`Dataset missing?`_) | |
| 40 | |
| 41 .. _gd_ped: ./static/formatHelp.html#gd_ped | |
| 42 .. _Dataset missing?: ./static/formatHelp.html | |
| 43 | |
| 44 ----- | |
| 45 | |
| 46 **What it does** | |
| 47 | |
| 48 The user selects a gd_ped dataset generated by the Prepare Input tool. | |
| 49 For all possible numbers K of ancestral | |
| 50 populations, from 1 up to a user-specified maximum, this tool produces values | |
| 51 that indicate how well the data can be explained as genotypes from individuals | |
| 52 derived from K ancestral populations. These values are computed by a 5-fold | |
| 53 cross-validation procedure, so that a good choice for K will exhibit a low | |
| 54 cross-validation error (CVE) compared with other potential settings for K. | |
| 55 | |
| 56 ----- | |
| 57 | |
| 58 **Acknowledgments** | |
| 59 | |
| 60 We use the program "Admixture", downloaded from | |
| 61 | |
| 62 http://www.genetics.ucla.edu/software/admixture/ | |
| 63 | |
| 64 and described in the paper "Fast model-based estimation of ancestry in | |
| 65 unrelated individuals" by David H. Alexander, John Novembre and Kenneth Lange, | |
| 66 Genome Research 19 (2009), pp. 1655-1664. Admixture is called with the "--cv" | |
| 67 flag to produce these values. | |
| 68 | |
| 69 ----- | |
| 70 | |
| 71 **Example** | |
| 72 | |
| 73 - output with max populations of 6:: | |
| 74 | |
| 75 CVE (K=1): 1.10120 | |
| 76 CVE (K=2): 1.34683 | |
| 77 CVE (K=3): 1.80611 | |
| 78 CVE (K=4): 1.96339 | |
| 79 CVE (K=5): 1.21522 | |
| 80 CVE (K=6): 0.51501 | |
| 81 | |
| 82 </help> | |
| 83 </tool> |