plink软件 --linear 对数量性状进行关联分析 SE计算

 

001、

root@DESKTOP-1N42TVH:/home/test4# ls
gwas_test.map  gwas_test.ped
root@DESKTOP-1N42TVH:/home/test4# plink --file gwas_test --linear --out test 1> /dev/null
root@DESKTOP-1N42TVH:/home/test4# ls
gwas_test.map  gwas_test.ped  test.assoc.linear  test.log
root@DESKTOP-1N42TVH:/home/test4# head test.assoc.linear
 CHR        SNP         BP   A1       TEST    NMISS       BETA         STAT            P
   1       snp1       2802    G        ADD      541     -8.911       -1.068        0.286
   1       snp2       2823    T        ADD      541      7.754        0.772       0.4405
   1       snp3       4512    G        ADD      541      9.264       0.9439       0.3456
   1       snp4      16529    T        ADD      541     -18.49       -1.711      0.08769
   1       snp5      16578    G        ADD      541      5.661       0.5701       0.5689
   1       snp6      16579    C        ADD      541     -5.577      -0.9858       0.3247
   1       snp7      16635    G        ADD      541      2.985       0.3425       0.7321
   1       snp8      20879    T        ADD      541      9.053        1.242       0.2148
   1       snp9      20908    C        ADD      541      9.278        1.386       0.1664
root@DESKTOP-1N42TVH:/home/test4# awk 'NR != 1 {print $(NF - 2)/$(NF - 1)}' test.assoc.linear | head
8.34363                           ## 计算SE
10.044
9.8146
10.8065
9.92984
5.65733
8.71533
7.28905
6.69408
7.62307
root@DESKTOP-1N42TVH:/home/test4# plink --file gwas_test --assoc --out test2 1> /dev/null  ## 验证
root@DESKTOP-1N42TVH:/home/test4# ls
gwas_test.map  gwas_test.ped  test.assoc.linear  test.log  test2.log  test2.qassoc
root@DESKTOP-1N42TVH:/home/test4# head -n 3 test2.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