plink --file hapmap1

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|         PLINK!       |    v0.99e     |    4/Jun/2006     |
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|  (C) 2006 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|       http://pngu.mgh.harvard.edu/purcell/plink/         |
@----------------------------------------------------------@
  
Writing this text to log file [ plink.log ]
Analysis started: Mon Jun  5 16:00:28 2006
 
Options in effect:
        --file hapmap1
 
83534 (of 83534) markers to be included from [ hapmap1.map ]
89 individuals read from [ hapmap1.ped ]
89 individuals with nonmissing phenotypes
Assuming a binary trait (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
Before frequency and genotyping pruning, there are 83534 SNPs
Applying filters (SNP-major mode)
89 founders and 0 non-founders found
0 of 89 individuals removed for low genotyping ( MIND > 0.1 )
Removing rare ( MAF < 0.01 ), low-genotyping ( MISS > 0.1 ) markers
After frequency and genotyping pruning, there are 65803 SNPs
Analysis finished: Mon Jun  5 16:00:38 2006
------------------------------------------------------------ /plink --file hapmap1 --make-bed --out hapmap1 83534 (of 83534) markers to be included from [ hapmap1.map ] 89 individuals read from [ hapmap1.ped ] 89 individuals with nonmissing phenotypes Assuming a binary trait (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 Before frequency and genotyping pruning, there are 83534 SNPs Applying filters (SNP-major mode) 89 founders and 0 non-founders found Removing rare ( MAF < 0 ), low-genotyping ( MISS > 1 ) markers After frequency and genotyping pruning, there are 83534 SNPs Writing pedigree information to [ hapmap1.fam ] Writing map (extended format) information to [ hapmap1.bim ] Writing genotype bitfile to [ hapmap1.bed ] Using (default) SNP-major mode Analysis finished: Mon Jun 5 16:01:33 2006 ------------------------------------------------------------ plink --bfile hapmap @----------------------------------------------------------@ | PLINK! | v0.99e | 4/Jun/2006 | |----------------------------------------------------------| | (C) 2006 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| | http://pngu.mgh.harvard.edu/purcell/plink/ | @----------------------------------------------------------@ *** PRE-RELEASE TRIAL VERSION *** Please visit the above website to check for more recent versions. Although this version is quite stable, there will inevitably still be a number of bugs that will be fixed (and features addded) in subsequent releases... Writing this text to log file [ plink.log ] Analysis started: Mon Jun 5 16:02:19 2006 Options in effect: --bfile hapmap1 Reading map (extended format) from [ hapmap1.bim ] 83534 markers to be included from [ hapmap1.bim ] Reading pedigree information from [ hapmap1.fam ] 89 individuals read from [ hapmap1.fam ] 89 individuals with nonmissing phenotypes Reading genotype bitfile from [ hapmap1.bed ] Detected that binary PED file is in SNP-major mode Before frequency and genotyping pruning, there are 83534 SNPs Applying filters (SNP-major mode) 89 founders and 0 non-founders found 0 of 89 individuals removed for low genotyping ( MIND > 0.1 ) Removing rare ( MAF < 0.01 ), low-genotyping ( MISS > 0.1 ) markers After frequency and genotyping pruning, there are 65803 SNPs Analysis finished: Mon Jun 5 16:02:21 2006 ------------------------------------------------------------ plink --bfile hapmap1 --missing 89 founders and 0 non-founders found 0 of 89 individuals removed for low genotyping ( MIND > 0.1 ) Writing individual missingness information to [ plink.imiss ] Writing locus missingness information to [ plink.lmiss ] Analysis finished: Mon Jun 5 16:02:57 2006 ------------------------------------------------------------ plink --bfile hapmap1 --freq ------------------------------------------------------------ plink --bfile hapmap1 --assoc --adjust ------------------------------------------------------------ plink --bfile hapmap1 --assoc --adjust ------------------------------------------------------------ plink --bfile hapmap1 --assoc --pheno qt.phe --perm --within uncon.cluster2 [shaun@faff asian]$ ~/src/plink2/plink --bfile hapmap1 --assoc --pheno qt.phe --perm --within uncon.cluster2 @----------------------------------------------------------@ | PLINK! | v0.99e | 4/Jun/2006 | |----------------------------------------------------------| | (C) 2006 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| | http://pngu.mgh.harvard.edu/purcell/plink/ | @----------------------------------------------------------@ *** PRE-RELEASE TRIAL VERSION *** Please visit the above website to check for more recent versions. Although this version is quite stable, there will inevitably still be a number of bugs that will be fixed (and features addded) in subsequent releases... Writing this text to log file [ plink.log ] Analysis started: Mon Jun 5 18:31:57 2006 Options in effect: --bfile hapmap1 --assoc --pheno qt.phe --perm --within uncon.cluster2 Reading map (extended format) from [ hapmap1.bim ] 83534 markers to be included from [ hapmap1.bim ] Reading pedigree information from [ hapmap1.fam ] 89 individuals read from [ hapmap1.fam ] 89 individuals with nonmissing phenotypes Reading genotype bitfile from [ hapmap1.bed ] Detected that binary PED file is in SNP-major mode Reading alternate phenotype from [ qt.phe ] Assuming a quantitative trait for alternate phenotype Missing phenotype is -9 89 individuals with non-missing alternate phenotype Reading clusters from [ uncon.cluster2 ] 89 of 89 individuals assigned to 45 cluster(s) Before frequency and genotyping pruning, there are 83534 SNPs Applying filters (SNP-major mode) 89 founders and 0 non-founders found 0 of 89 individuals removed for low genotyping ( MIND > 0.1 ) Removing rare ( MAF < 0.01 ), low-genotyping ( MISS > 0.1 ) markers After frequency and genotyping pruning, there are 65803 SNPs Set to permute within 45 cluster(s) Writing QT association results to [ plink.qassoc ] Adaptive permutation: 1000000 of (max) 1000000 : 25 SNPs left Writing permutation association results to [ plink.assoc.perm ] Analysis finished: Mon Jun 5 19:22:02 2006 CHR SNP CHISQ P EMP1 NP 2 rs2222162 42.01 9.083e-11 1e-06 1000000 6 rs1606447 5.869 0.01541 5.206e-05 38415 10 rs1393829 16.34 5.288e-05 0.0001896 10549 21 rs219746 27.49 1.581e-07 0.0001896 10549 2 rs2304287 9.021 0.00267 0.0001896 10549 6 rs2326873 6.659 0.009865 0.0001896 10549 2 rs1385855 7.59 0.00587 0.0002227 13468 2 rs6543704 8.131 0.00435 0.0002227 13468 2 rs6752439 16.88 3.976e-05 0.0002227 13468 5 rs1651350 4.522 0.03347 0.0002227 13468 9 rs1434874 4.104 0.04278 0.0002484 16099 11 rs11226452 3.809 0.05099 0.0002699 18525 11 rs7119997 3.809 0.05099 0.0002699 18525 12 rs1347015 5.727 0.01671 0.0002883 20811 12 rs2520567 5.153 0.0232 0.0002883 20811 14 rs1190968 5.461 0.01945 0.0002883 20811 2 rs2176427 11.52 0.00069 0.0003188 25090 6 rs9400564 4.902 0.02682 0.0003317 27132 2 rs4853112 5.811 0.01592 0.0003544 31040 15 rs4777075 5.535 0.01864 0.0003644 32934 7 rs2288970 12.46 0.0004161 0.0003737 34790 13 rs7999500 13.1 0.0002958 0.0003822 36630 18 rs6506386 17.48 2.896e-05 0.0003905 38415 9 rs324517 8.219 0.004145 0.0004754 63104 10 rs10795055 8.83 0.002964 0.0005146 79680 10 rs705458 8.83 0.002964 0.0005146 79680 9 rs10780262 8.602 0.003358 0.0005146 79680 10 rs4934208 2.744 0.0976 0.0005174 81180 11 rs11028504 2.943 0.08625 0.0005174 81180 17 rs3760219 3.983 0.04595 0.0005464 97000 11 rs748923 5.03 0.02491 0.0005551 102691 3 rs6792701 3.172 0.07493 0.0005594 105470 4 rs6840352 4.902 0.02683 0.0005613 106893 2 rs1374163 12.19 0.0004806 0.0005873 126000 14 rs8010088 4.111 0.04259 0.0005889 127360 8 rs951702 9.204 0.002415 0.0006209 157842 9 rs1332473 9.652 0.001892 0.0006356 174650 19 rs998900 2.998 0.08337 0.0006506 195216 13 rs4242927 13.48 0.0002411 0.000684 250000 19 rs277444 4.293 0.03826 0.0006996 284430 3 rs3908140 9.998 0.001567 0.000742 407000 8 rs7008494 9.35 0.00223 0.0007492 435128 10 rs7081349 2.631 0.1048 0.0007655 509490 22 rs5748391 5.229 0.02222 0.000774 553000 1 rs2312237 6.628 0.01004 0.0007916 667000 ------------------------------------------------------------ plink --bfile hapmap1 --from rs222612 --to rs222612 --recodeAD ------------------------------------------------------------- simulation rs2222162 is key SNP > table(x , d$rs2222162_A , k ) , , k = 1 x 0 1 2 1 7 21 6 2 0 0 11 , , k = 2 x 0 1 2 1 10 1 0 2 3 19 11 > > > table(x , k, d$rs2222162_A ) , , = 0 k x 1 2 1 7 10 2 0 3 , , = 1 k x 1 2 1 21 1 2 0 19 , , = 2 k x 1 2 1 6 0 2 11 11