plink 软件 --assoc 数量性状关联分析 T值的来源

 

001、

root@DESKTOP-1N42TVH:/home/test4# ls
gwas_test.map  gwas_test.ped
root@DESKTOP-1N42TVH:/home/test4# plink --file gwas_test --assoc --out test 1> /dev/null
root@DESKTOP-1N42TVH:/home/test4# ls
gwas_test.map  gwas_test.ped  test.log  test.qassoc
root@DESKTOP-1N42TVH:/home/test4# head test.qassoc
 CHR        SNP         BP    NMISS       BETA         SE         R2        T            P
   1       snp1       2802      541     -8.911      8.344   0.002111   -1.068        0.286
   1       snp2       2823      541      7.754      10.04   0.001104    0.772       0.4405
   1       snp3       4512      541      9.264      9.814    0.00165   0.9439       0.3456
   1       snp4      16529      541     -18.49      10.81   0.005401   -1.711      0.08769
   1       snp5      16578      541      5.661       9.93  0.0006026   0.5701       0.5689
   1       snp6      16579      541     -5.577      5.657     0.0018  -0.9858       0.3247
   1       snp7      16635      541      2.985      8.717  0.0002176   0.3425       0.7321
   1       snp8      20879      541      9.053       7.29   0.002853    1.242       0.2148
   1       snp9      20908      541      9.278      6.695    0.00355    1.386       0.1664
root@DESKTOP-1N42TVH:/home/test4# awk 'NR != 1 {print $5/$6}' test.qassoc | head   ## BETA除以SE
-1.06795
0.772311
0.943958
-1.71045
0.570091
-0.985858
0.342434
1.24184
1.38581
-2.72167