plink软件 --linear 对数量性状进行关联分析 SE计算
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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