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/test-data/rgTDTtest1_TDT_log.txt

https://bitbucket.org/cistrome/cistrome-harvard/
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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