/test-data/rgTDTtest1_TDT_log.txt
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1 2@----------------------------------------------------------@ 3| PLINK! | v1.07 | 10/Aug/2009 | 4|----------------------------------------------------------| 5| (C) 2009 Shaun Purcell, GNU General Public License, v2 | 6|----------------------------------------------------------| 7| For documentation, citation & bug-report instructions: | 8| http://pngu.mgh.harvard.edu/purcell/plink/ | 9@----------------------------------------------------------@ 10 11Skipping web check... [ --noweb ] 12Writing this text to log file [ rgTDTtest1.log ] 13Analysis started: Sun May 9 21:23:49 2010 14 15Options in effect: 16 --noweb 17 --bfile /share/shared/galaxy/test-data/tinywga 18 --out rgTDTtest1 19 --mind 0.5 20 --tdt 21 22Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 2325 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] 24Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 2540 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 2640 individuals with nonmissing phenotypes 27Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 28Missing phenotype value is also -9 2910 cases, 30 controls and 0 missing 3021 males, 19 females, and 0 of unspecified sex 31Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 32Detected that binary PED file is v1.00 SNP-major mode 33Before frequency and genotyping pruning, there are 25 SNPs 3427 founders and 13 non-founders found 350 of 40 individuals removed for low genotyping ( MIND > 0.5 ) 36Total genotyping rate in remaining individuals is 0.995 370 SNPs failed missingness test ( GENO > 1 ) 380 SNPs failed frequency test ( MAF < 0 ) 39After frequency and genotyping pruning, there are 25 SNPs 40After filtering, 10 cases, 30 controls and 0 missing 41After filtering, 21 males, 19 females, and 0 of unspecified sex 4214 nuclear families, 1 founder singletons found 4313 non-founders with 2 parents in 13 nuclear families 440 non-founders without 2 parents in 0 nuclear families 4510 affected offspring trios 460 phenotypically discordant parent pairs found 47Converting data to Individual-major format 480 Mendel errors detected in total 49Writing TDT results (asymptotic) to [ rgTDTtest1.tdt ] 50 51Analysis finished: Sun May 9 21:23:49 2010 52 53###maxp=0.590405,minp=-0.000000,prange=1.090405,scalefact=917.090439