使用 emmax 进行GWAS分析
作者：互联网
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
标签：分析,GWAS,plink,format,kin,test,home,emmax 来源： https://www.cnblogs.com/liujiaxin2018/p/16536315.html