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/test-data/rgCaCotest1_CaCo_log.txt

https://bitbucket.org/cistrome/cistrome-harvard/
Plain Text | 46 lines | 40 code | 6 blank | 0 comment | 0 complexity | 92cb93952c385ab25b25c42c797bc039 MD5 | raw file
 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 [ rgCaCotest1.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 rgCaCotest1
19	--model
20
21Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 
2225 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
23Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 
2440 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 
2540 individuals with nonmissing phenotypes
26Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
27Missing phenotype value is also -9
2810 cases, 30 controls and 0 missing
2921 males, 19 females, and 0 of unspecified sex
30Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 
31Detected that binary PED file is v1.00 SNP-major mode
32Before frequency and genotyping pruning, there are 25 SNPs
3327 founders and 13 non-founders found
34Total genotyping rate in remaining individuals is 0.995
350 SNPs failed missingness test ( GENO > 1 )
360 SNPs failed frequency test ( MAF < 0 )
37After frequency and genotyping pruning, there are 25 SNPs
38After filtering, 10 cases, 30 controls and 0 missing
39After filtering, 21 males, 19 females, and 0 of unspecified sex
40Full-model association tests, minimum genotype count: --cell 5
41Writing full model association results to [ rgCaCotest1.model ] 
42
43Analysis finished: Sun May  9 21:23:49 2010
44
45###maxp=0.667360,minp=-0.000000,prange=1.167360,scalefact=856.633772
46Rgenetics V000.1 April 2007 http://rgenetics.org Galaxy Tools, rgCaCo.py started 09/05/2010 21:23:49