使用 emmax 进行GWAS分析
001、
root@PC1:/home/test# ls gwas_test.map gwas_test.ped root@PC1:/home/test# plink --file gwas_test --recode 12 transpose --out emmax_format 1> /dev/null root@PC1:/home/test# ls emmax_format.log emmax_format.tfam emmax_format.tped gwas_test.map gwas_test.ped root@PC1:/home/test# plink --file gwas_test --pca 3 1> /dev/null root@PC1:/home/test# ls emmax_format.log emmax_format.tfam emmax_format.tped gwas_test.map gwas_test.ped plink.eigenval plink.eigenvec plink.log root@PC1:/home/test# awk '{print $1, $2, $6}' gwas_test.ped > phenotype.txt root@PC1:/home/test# awk '{print $1, $2, 1, $3, $4, $5}' plink.eigenvec > cov.file root@PC1:/home/test# ls cov.file emmax_format.tfam gwas_test.map phenotype.txt plink.eigenvec emmax_format.log emmax_format.tped gwas_test.ped plink.eigenval plink.log root@PC1:/home/test# /home/software/emmax-kin-intel64 emmax_format -v -d 10 -o emmax_kin 1> /dev/null Reading TFAM file emmax_format.tfam .... Memory allocated, nrows = 541, nheadercols = 6, nvaluecols = 0 Freeing cmat Freeing cheaders Memory freed Identified 541 individuals from TFAM file Setting # unit lines = 923672 to fit the memory requirement Reading TPED file emmax_format.tped .... Reading 0 SNPs Reading 10000 SNPs Reading 20000 SNPs Reading 30000 SNPs Reading 40000 SNPs Reading 50000 SNPs Reading 60000 SNPs Reading 70000 SNPs Reading 80000 SNPs Reading 90000 SNPs Reading 100000 SNPs Succesfully finished reading TPED file Computing kinship matrix with the remaining 101549 SNPs.. f_block_weight = 101549.000000 nex = 0 nex_call_rate = 0 OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. ## AMD处理器 OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". Finished computing kinship matrix Printing the kinship matrix to file emmax_format.
002、使用kin关系
root@PC1:/home/test# ls cov.file emmax_format.tfam emmax_kin gwas_test.ped plink.eigenval plink.log emmax_format.log emmax_format.tped gwas_test.map phenotype.txt plink.eigenvec root@PC1:/home/test# /home/software/emmax-intel64 -t emmax_format -o emmax_kin -p phenotype.txt -k emmax_kin nmiss = 0 , mphenoflag = 0 OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". evals[0] = -0.000000, evals[1] = 1.008034, evals[n-1] = 6.654231 k = 540, n-q = 540 root@PC1:/home/test# ls cov.file emmax_format.tfam emmax_kin emmax_kin.ps gwas_test.map phenotype.txt plink.eigenvec emmax_format.log emmax_format.tped emmax_kin.log emmax_kin.reml gwas_test.ped plink.eigenval plink.log root@PC1:/home/test# head emmax_kin.ps snp1 -1.1141 7.9858 0.8891 snp2 -5.6218 9.4275 0.55121 snp3 -8.9421 9.2048 0.33176 snp4 2.9532 10.513 0.77888 snp5 2.3625 8.9748 0.79247 snp6 -3.3411 5.1728 0.51862 snp7 -3.8305 8.1569 0.63883 snp8 0.94697 6.9264 0.8913 snp9 0.57514 6.2112 0.92626 snp10 4.5423 7.4249 0.54095
003、使用kin + cov协变量
root@PC1:/home/test# ls cov.file emmax_format.tfam emmax_kin emmax_kin.ps gwas_test.map phenotype.txt plink.eigenvec emmax_format.log emmax_format.tped emmax_kin.log emmax_kin.reml gwas_test.ped plink.eigenval plink.log root@PC1:/home/test# /home/software/emmax-intel64 -t emmax_format -o emmax_kin_cov -p phenotype.txt -k emmax_kin -c cov.file nmiss = 0 , mphenoflag = 0 OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.204020 k = 537, n-q = 537 root@PC1:/home/test# ls cov.file emmax_format.tped emmax_kin_cov.ps emmax_kin.ps gwas_test.ped plink.eigenvec emmax_format.log emmax_kin emmax_kin_cov.reml emmax_kin.reml phenotype.txt plink.log emmax_format.tfam emmax_kin_cov.log emmax_kin.log gwas_test.map plink.eigenval root@PC1:/home/test# head emmax_kin_cov.ps snp1 -2.1373 7.8752 0.78619 snp2 -5.258 9.3224 0.57298 snp3 -8.9221 9.0994 0.32728 snp4 -0.49211 10.405 0.9623 snp5 4.4257 8.9895 0.6227 snp6 -2.9939 5.1511 0.56134 snp7 -4.8139 8.0663 0.5509 snp8 -0.83212 6.858 0.90347 snp9 1.8465 6.2003 0.76596 snp10 2.6951 7.3799 0.71511
参考:
01、https://www.jianshu.com/p/0f39ff5a7643
02、https://zhuanlan.zhihu.com/p/270092364