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