gemma 对 数量性状 一般线性模型关联分析计算 T值

 

001、

root@DESKTOP-1N42TVH:/home/test4# ls
gwas_test.bed  gwas_test.bim  gwas_test.fam
root@DESKTOP-1N42TVH:/home/test4# /home/software/gemma-0.98.5-linux-static-AMD64 -bfile gwas_test -gk -o kin 1> /dev/null
**** INFO: Done.
root@DESKTOP-1N42TVH:/home/test4# ls
gwas_test.bed  gwas_test.bim  gwas_test.fam  output
root@DESKTOP-1N42TVH:/home/test4# /home/software/gemma-0.98.5-linux-static-AMD64 -bfile gwas_test -k output/kin.cXX.txt -lm -o result 1> /dev/null
**** INFO: Done.
root@DESKTOP-1N42TVH:/home/test4# ls
gwas_test.bed  gwas_test.bim  gwas_test.fam  output
root@DESKTOP-1N42TVH:/home/test4# cd output/
root@DESKTOP-1N42TVH:/home/test4/output# ls
kin.cXX.txt  kin.log.txt  result.assoc.txt  result.log.txt
root@DESKTOP-1N42TVH:/home/test4/output# head -n 5 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
root@DESKTOP-1N42TVH:/home/test4/output# awk 'NR != 1 {print $(NF - 2)/$(NF - 1)}' result.assoc.txt | head -n 5
-1.06793
0.77199
0.943913
-1.71083
0.570069
root@DESKTOP-1N42TVH:/home/test4/output# cd ..
root@DESKTOP-1N42TVH:/home/test4# plink --bfile gwas_test --assoc --out test 1> /dev/null
root@DESKTOP-1N42TVH:/home/test4# ls
gwas_test.bed  gwas_test.bim  gwas_test.fam  output  test.log  test.qassoc
root@DESKTOP-1N42TVH:/home/test4# head -n 5 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