Post by vsab on Apr 9, 2015 10:47:31 GMT
Hi there
I am using GCTA to conduct mmla because it allows me to incorporate a relationship matrix as i have related individuals (not family data).
I want to inlcude age, sex and PCA's in the analysis but i am struggling as to how to do it. Previous posts have suggested adjusting the phenotype for covariates (age and sex) prior to the running the flag mlma. What are the commands that i use and how should i construct the files, 2 separate because one is discrete and the other (age) is quantitative...
gcta64
--bfile [plinkfile]
--make-grm
--maf [e.g. 0.01]
--out[filename]
gcta64
--grm [filename]
--pca 10
--out [filename]
gcta64
--mlma
--bfile [plinkfile]
--grm [filename]
--pheno [filename.phen]
--mpheno [#]
--qcovar [filename.eigenvec]
--out
Where in the commands do i adjust the GRM for the other covariates i.e age and sex?
Please help. I am just starting out with GCTA
I am using GCTA to conduct mmla because it allows me to incorporate a relationship matrix as i have related individuals (not family data).
I want to inlcude age, sex and PCA's in the analysis but i am struggling as to how to do it. Previous posts have suggested adjusting the phenotype for covariates (age and sex) prior to the running the flag mlma. What are the commands that i use and how should i construct the files, 2 separate because one is discrete and the other (age) is quantitative...
gcta64
--bfile [plinkfile]
--make-grm
--maf [e.g. 0.01]
--out[filename]
gcta64
--grm [filename]
--pca 10
--out [filename]
gcta64
--mlma
--bfile [plinkfile]
--grm [filename]
--pheno [filename.phen]
--mpheno [#]
--qcovar [filename.eigenvec]
--out
Where in the commands do i adjust the GRM for the other covariates i.e age and sex?
Please help. I am just starting out with GCTA
