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
