可以用默认的mlma模型计算 ##--mlma ##--mpheno 1 默认为1,表示取第三列为表型;如果是2,则表示取第四列为表型,以此类推 gcta64 --mlma --bfile test --grm test --qcovar test.eigenvec --mpheno 1 --pheno test.pheno --out test --thread-num 10 ##--grm test中的test文件来自3.1中 ##-...
MLMA和MLMA-LOCO:稠密矩阵的LMM模型 COJO:条件和联合分析 mtCOJO:多性状条件和联合分析 fastBAT: fastGWA-BB: ACTA-V: 2.3 GWAS数据模拟,群体遗传和孟德尔随机化 模拟GWAS数据 GSMR:孟德尔随机化 PCA和Fst计算 计算近交系数 计算LD 3. 常见问题 1,样本量少的话遗传力异常 遗传力会是0或者1,标准误很大,不正常...
这里,分享一下常用GWAS软件,比如GAPIT,GEMMA,GCTA是如何计算显著SNP解释百分比(PVE)的。 1. 参考文献 首先是这个论坛的内容:How to determine the percent phenotypic variation explained (PVE) by a selected SNP? ❝ Feofanova, Elena. (2020). Re: How to determine the percent phenotypic variation explained...
MLMA and MLMA-LOCO: mixed linear model association analysis using a dense GRM; COJO: conditional & joint association analysis using GWAS summary statistics; mtCOJO: multi-trait-based conditional & joint association analysis using GWAS summary statistics; ...
Contributions to the development of the methods implemented in GCTA (e.g., GREML methods, COJO, mtCOJO, MLMA-LOCO, fastBAT, fastGWA and fastGWA-GLMM) can be found in the corresponding publications (https://yanglab.westlake.edu.cn/software/gcta/index.html#Overview). ...
Contributions to the development of the methods implemented in GCTA (e.g., GREML methods, COJO, mtCOJO, MLMA-LOCO, fastBAT, fastGWA and fastGWA-GLMM) can be found in the corresponding publications (https://yanglab.westlake.edu.cn/software/gcta/index.html#Overview). ...