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1 <tool id="hgv_snpFreq" name="snpFreq" version="1.0.0">
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2 <description>significant SNPs in case-control data</description>
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3
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4 <command interpreter="perl">
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5 snpFreq2.pl $input $group1_1 $group1_2 $group1_3 $group2_1 $group2_2 $group2_3 0.05 $output
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6 </command>
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7
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8 <inputs>
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9 <param format="tabular" name="input" type="data" label="Dataset" />
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10 <param name="group1_1" label="Column with genotype 1 count for group 1" type="data_column" data_ref="input" />
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11 <param name="group1_2" label="Column with genotype 2 count for group 1" type="data_column" data_ref="input" />
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12 <param name="group1_3" label="Column with genotype 3 count for group 1" type="data_column" data_ref="input" />
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13 <param name="group2_1" label="Column with genotype 1 count for group 2" type="data_column" data_ref="input" />
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14 <param name="group2_2" label="Column with genotype 2 count for group 2" type="data_column" data_ref="input" />
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15 <param name="group2_3" label="Column with genotype 3 count for group 2" type="data_column" data_ref="input" />
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16 </inputs>
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17
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18 <outputs>
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19 <data format="tabular" name="output" />
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20 </outputs>
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21
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22 <requirements>
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23 <requirement type="binary">R</requirement>
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24 </requirements>
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25
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26 <tests>
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27 <test>
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28 <param name="input" ftype="tabular" value="snpFreqInput.txt" dbkey="hg18" />
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29 <param name="group1_1" value="4" />
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30 <param name="group1_2" value="5" />
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31 <param name="group1_3" value="6" />
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32 <param name="group2_1" value="7" />
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33 <param name="group2_2" value="8" />
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34 <param name="group2_3" value="9" />
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35 <output name="output" file="snpFreqTestOut.txt" />
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36 </test>
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37 </tests>
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38
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39 <help>
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40
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41 **Dataset formats**
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42
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43 The input is tabular_, with six columns of allele counts. The output is also tabular,
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44 and includes all of the input data plus the additional columns described below.
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45 (`Dataset missing?`_)
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46
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47 .. _tabular: ./static/formatHelp.html#tab
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48 .. _Dataset missing?: ./static/formatHelp.html
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49
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50 -----
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51
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52 **What it does**
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53
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54 This tool performs a basic analysis of bi-allelic SNPs in case-control
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55 data, using the R statistical environment and Fisher's exact test to
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56 identify SNPs with a significant difference in the allele frequencies
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57 between the two groups. R's "qvalue" package is used to correct for
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58 multiple testing.
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59
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60 The input file includes counts for each allele combination (AA aa Aa)
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61 for each group at each SNP position. The assignment of codes (1 2 3)
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62 to these genotypes is arbitrary, as long as it is consistent for both
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63 groups. Any other input columns are ignored in the computation, but
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64 are copied to the output. The output appends eight additional columns,
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65 namely the minimum expected counts of the three genotypes for each
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66 group, the p-value, and the q-value.
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67
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68 -----
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69
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70 **Example**
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71
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72 - input file::
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73
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74 chr1 210 211 38 4 15 56 0 1 x
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75 chr1 228 229 55 0 2 56 0 1 x
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76 chr1 230 231 46 0 11 55 0 2 x
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77 chr1 234 235 43 0 14 55 0 2 x
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78 chr1 236 237 55 0 2 13 10 34 x
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79 chr1 437 438 55 0 2 46 0 11 x
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80 chr1 439 440 56 0 1 55 0 2 x
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81 chr1 449 450 56 0 1 13 20 24 x
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82 chr1 518 519 56 0 1 38 4 15 x
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83
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84 Here the group 1 genotype counts are in columns 4 - 6, while those
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85 for group 2 are in columns 7 - 9.
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86
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87 Note that the "x" column has no meaning. It was added to this example
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88 to show that extra columns can be included, and to make it easier
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89 to see where the new columns are appended in the output.
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90
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91 - output file::
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92
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93 chr1 210 211 38 4 15 56 0 1 x 47 2 8 47 2 8 1.50219088598917e-05 6.32501425679652e-06
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94 chr1 228 229 55 0 2 56 0 1 x 55.5 0 1.5 55.5 0 1.5 1 0.210526315789474
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95 chr1 230 231 46 0 11 55 0 2 x 50.5 0 6.5 50.5 0 6.5 0.0155644201009862 0.00409590002657532
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96 chr1 234 235 43 0 14 55 0 2 x 49 0 8 49 0 8 0.00210854461554067 0.000739840215979182
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97 chr1 236 237 55 0 2 13 10 34 x 34 5 18 34 5 18 6.14613878554783e-17 4.31307984950725e-17
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98 chr1 437 438 55 0 2 46 0 11 x 50.5 0 6.5 50.5 0 6.5 0.0155644201009862 0.00409590002657532
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99 chr1 439 440 56 0 1 55 0 2 x 55.5 0 1.5 55.5 0 1.5 1 0.210526315789474
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100 chr1 449 450 56 0 1 13 20 24 x 34.5 10 12.5 34.5 10 12.5 2.25757007974134e-18 2.37638955762246e-18
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101 chr1 518 519 56 0 1 38 4 15 x 47 2 8 47 2 8 1.50219088598917e-05 6.32501425679652e-06
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102
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103 </help>
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104 </tool>
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