Source

Cistrome-Harvard / test-data / rgTDTtest1_TDT_log.txt

The default branch has multiple heads

Full commit

@----------------------------------------------------------@
|        PLINK!       |     v1.07      |   10/Aug/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ] 
Writing this text to log file [ rgTDTtest1.log ]
Analysis started: Sun May  9 21:23:49 2010

Options in effect:
	--noweb
	--bfile /share/shared/galaxy/test-data/tinywga
	--out rgTDTtest1
	--mind 0.5
	--tdt

Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 
25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 
40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 
40 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
10 cases, 30 controls and 0 missing
21 males, 19 females, and 0 of unspecified sex
Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 
Detected that binary PED file is v1.00 SNP-major mode
Before frequency and genotyping pruning, there are 25 SNPs
27 founders and 13 non-founders found
0 of 40 individuals removed for low genotyping ( MIND > 0.5 )
Total genotyping rate in remaining individuals is 0.995
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 25 SNPs
After filtering, 10 cases, 30 controls and 0 missing
After filtering, 21 males, 19 females, and 0 of unspecified sex
14 nuclear families, 1 founder singletons found
13 non-founders with 2 parents in 13 nuclear families
0 non-founders without 2 parents in 0 nuclear families
10 affected offspring trios
0 phenotypically discordant parent pairs found
Converting data to Individual-major format
0 Mendel errors detected in total
Writing TDT results (asymptotic) to [ rgTDTtest1.tdt ] 

Analysis finished: Sun May  9 21:23:49 2010

###maxp=0.590405,minp=-0.000000,prange=1.090405,scalefact=917.090439