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2 | @----------------------------------------------------------@ |
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3 | | PLINK! | v1.07 | 10/Aug/2009 | |
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4 | |----------------------------------------------------------| |
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5 | | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |
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6 | |----------------------------------------------------------| |
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7 | | For documentation, citation & bug-report instructions: | |
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8 | | http://pngu.mgh.harvard.edu/purcell/plink/ | |
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9 | @----------------------------------------------------------@ |
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10 | |
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11 | Skipping web check... [ --noweb ] |
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12 | Writing this text to log file [ rgTDTtest1.log ] |
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13 | Analysis started: Sun May 9 21:23:49 2010 |
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14 | |
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15 | Options in effect: |
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16 | --noweb |
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17 | --bfile /share/shared/galaxy/test-data/tinywga |
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18 | --out rgTDTtest1 |
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19 | --mind 0.5 |
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20 | --tdt |
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21 | |
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22 | Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] |
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23 | 25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] |
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24 | Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] |
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25 | 40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] |
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26 | 40 individuals with nonmissing phenotypes |
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27 | Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) |
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28 | Missing phenotype value is also -9 |
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29 | 10 cases, 30 controls and 0 missing |
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30 | 21 males, 19 females, and 0 of unspecified sex |
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31 | Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] |
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32 | Detected that binary PED file is v1.00 SNP-major mode |
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33 | Before frequency and genotyping pruning, there are 25 SNPs |
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34 | 27 founders and 13 non-founders found |
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35 | 0 of 40 individuals removed for low genotyping ( MIND > 0.5 ) |
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36 | Total genotyping rate in remaining individuals is 0.995 |
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37 | 0 SNPs failed missingness test ( GENO > 1 ) |
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38 | 0 SNPs failed frequency test ( MAF < 0 ) |
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39 | After frequency and genotyping pruning, there are 25 SNPs |
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40 | After filtering, 10 cases, 30 controls and 0 missing |
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41 | After filtering, 21 males, 19 females, and 0 of unspecified sex |
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42 | 14 nuclear families, 1 founder singletons found |
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43 | 13 non-founders with 2 parents in 13 nuclear families |
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44 | 0 non-founders without 2 parents in 0 nuclear families |
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45 | 10 affected offspring trios |
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46 | 0 phenotypically discordant parent pairs found |
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47 | Converting data to Individual-major format |
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48 | 0 Mendel errors detected in total |
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49 | Writing TDT results (asymptotic) to [ rgTDTtest1.tdt ] |
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50 | |
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51 | Analysis finished: Sun May 9 21:23:49 2010 |
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52 | |
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53 | ###maxp=0.590405,minp=-0.000000,prange=1.090405,scalefact=917.090439 |
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