gemma、plink使用一般线性模型进行GWAS分析

 

001、测试数据

root@DESKTOP-1N42TVH:/home/test# ls        ## 表型数据为ped文件的第6列
gwas_test.map  gwas_test.ped

 

002、plink 一般线性模型GWAS

（1）、

root@DESKTOP-1N42TVH:/home/test# ls
gwas_test.map  gwas_test.ped
root@DESKTOP-1N42TVH:/home/test# plink --file gwas_test --assoc --out result
root@DESKTOP-1N42TVH:/home/test# ls
gwas_test.map  gwas_test.ped  result.log  result.qassoc
root@DESKTOP-1N42TVH:/home/test# head result.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

 

（2）

root@DESKTOP-1N42TVH:/home/test# ls
gwas_test.map  gwas_test.ped
root@DESKTOP-1N42TVH:/home/test# plink --file gwas_test --linear --out result
root@DESKTOP-1N42TVH:/home/test# ls
gwas_test.map  gwas_test.ped  result.assoc.linear  result.log
root@DESKTOP-1N42TVH:/home/test# head result.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

 

 

 

003、gemma 一般线性模型GWAS分析

root@DESKTOP-1N42TVH:/home/test# ls
gwas_test.bed  gwas_test.bim  gwas_test.fam    ## 二进制文件
root@DESKTOP-1N42TVH:/home/test# /home/software/gemma-0.98.5-linux-static-AMD64 -bfile gwas_test -gk -o kin
root@DESKTOP-1N42TVH:/home/test# /home/software/gemma-0.98.5-linux-static-AMD64 -bfile gwas_test -k output/kin.cXX.txt -lm -o result
root@DESKTOP-1N42TVH:/home/test# head output/result.assoc.txt
chr     rs      ps      n_mis   n_obs   allele1 allele0 af      beta    se      p_wald
1       snp1    2802    0       541     G       T       0.099   -8.911279e+00   8.344418e+00    2.860288e-01
1       snp2    2823    0       541     T       C       0.063   7.753729e+00    1.004382e+01    4.404589e-01
1       snp3    4512    0       541     G       A       0.067   9.263943e+00    9.814405e+00    3.456371e-01
1       snp4    16529   0       541     T       C       0.055   -1.848994e+01   1.080760e+01    8.768826e-02
1       snp5    16578   0       541     G       C       0.065   5.661041e+00    9.930443e+00    5.688682e-01
1       snp6    16579   0       541     C       A       0.275   -5.577146e+00   5.657429e+00    3.246690e-01
1       snp7    16635   0       541     G       C       0.088   2.985488e+00    8.716807e+00    7.321098e-01
1       snp8    20879   0       541     T       G       0.130   9.052785e+00    7.289524e+00    2.148173e-01
1       snp9    20908   0       541     C       T       0.167   9.277698e+00    6.695314e+00    1.664115e-01