Stark
New Member
Posts: 6
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Post by Stark on Dec 17, 2015 10:08:06 GMT
i am doing a gwas of a disease trait(code 0/1), i want to correct fixed effect in the model of association analysis,should i prepare a .covar file include the fixed effect? When i using the "--mlma-no-adj-covar" to adjust the fixed effect it doesn't have a result. my sciprt like this "./gcta64 --mlma-no-adj-covar --bfile gcta_maf0.01 --grm maf0.01 -- covar gcta_maf0.01.covar --pheno maf0.01.phen --out gcta_maf0.01",is this options has problem? the attachments is my log file myGCTA.txt (928 B)and .covarfile gcta_maf0.01.covar (66.66 KB) anybody can help me?please
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Post by Jian Yang on Dec 18, 2015 1:40:19 GMT
You might need to add --mlma option.
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Stark
New Member
Posts: 6
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Post by Stark on Dec 18, 2015 6:55:40 GMT
You might need to add --mlma option. all right,i add the --mlma option before the --mlma-no-adj-covar and also behind the --mlma-no-adj-covar,still doesn't have a result this is my log file: Analysis started: Fri Dec 18 10:04:42 2015 Options: --mlma --mlma-no-adj-covar --bfile gcta_maf0.01 --grm maf0.01 --covar gcta_maf0.01.covar --pheno maf0.01.phen --out gcta_maf0.01 Note: This is a multi-thread program. You could specify the number of threads by the --thread-num option to speed up the computation if there are multiple processors in your machine. Reading PLINK FAM file from [gcta_maf0.01.fam]. 2592 individuals to be included from [gcta_maf0.01.fam]. Reading PLINK BIM file from [gcta_maf0.01.bim]. 44046 SNPs to be included from [gcta_maf0.01.bim]. Reading PLINK BED file from [gcta_maf0.01.bed] in SNP-major format ... Genotype data for 2592 individuals and 44046 SNPs to be included from [gcta_maf0.01.bed]. Reading phenotypes from [maf0.01.phen]. Non-missing phenotypes of 2592 individuals are included from [maf0.01.phen]. Reading discrete covariate(s) from [gcta_maf0.01.covar]. 1 discrete covariate(s) of 2592 individuals are included from [gcta_maf0.01.covar]. Reading IDs of the GRM from [maf0.01.grm.id]. Analysis finished: Fri Dec 18 10:04:44 2015 Computational time: 0:0:2
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Post by Jian Yang on Dec 21, 2015 1:19:54 GMT
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Stark
New Member
Posts: 6
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Post by Stark on Dec 21, 2015 9:57:21 GMT
Thank you very much for your reply .I have changed the format of covariate file ,it's still not working.So now i am trying to adjust phenotype,but i have another question for the binary trait. how can adjust the phenotype suitable?should i use the logistic model,how to adjust the phenotype in R?Can you give me some directions? Thanks again.
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