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* Once --kinGeno --kinSave --prefix options are requested, you would expect to see a GRM generated (compressed by gzip) with name yourprefix.Empirical.Kinship.gz. If --prefix option is not used, then the file name is Empirical.Kinship.gz.
* Once --kinGeno --kinSave --prefix options are requested, you would expect to see a GRM generated (compressed by gzip) with name yourprefix.Empirical.Kinship.gz. If --prefix option is not used, then the file name is Empirical.Kinship.gz.
* If --vcX --kinGeno --kinSave --prefix options are requested, besides the autosomal GRM, you would also expect to see a separate GRM for chromosome X saved (compressed by gzip also) under the name yourprefix.Empirical.KinshipX.gz.
* If --vcX --kinGeno --kinSave --prefix options are requested, besides the autosomal GRM, you would also expect to see a separate GRM for chromosome X saved (compressed by gzip also) under the name yourprefix.Empirical.KinshipX.gz.
* The GRMs are generated based on all genotyped individuals included in the PED file; samples with missing phenotype or missing covariates are not excluded from GRMs. This feature makes GRMs reusable if you have multiple traits to analyze in separate runs. You can simple use --kinFile option (--kinxFile option if you have X chromosome GRM together with --vcX option issued) to reuse the pre-saved GRMs.
* The GRMs are generated based on all genotyped individuals included in the PED file; samples with missing phenotype or missing covariates are not excluded from GRMs. This feature makes GRMs reusable if you have multiple traits to analyze in separate runs. You can simplely use --kinFile option (--kinxFile option if you have X chromosome GRM together with --vcX option issued) to reuse the pre-saved GRMs.
* The format for both autosomal and chromosome X GRMs are the same. The first row has all sample IDs (sample size=N) listed. The rest of the file is a symmetric matrix with dimention ''NxN'', and element ''ij'' of this matrix represents the kinship between the <math>i^{th}</math> and the <math>j^{th}</math> sample whose ID can be found from the first row.
* The format for both autosomal and chromosome X GRMs are the same. The first row has all sample IDs (sample size=N) listed. The rest of the file is a symmetric matrix with dimention ''NxN'', and element ''ij'' of this matrix represents the kinship between the <math>i^{th}</math> and the <math>j^{th}</math> sample whose ID can be found from the first row.
* For details about GRM calculation, please refer to [[RAREMETALWORKER_method | '''method''']].
* For details about GRM calculation, please refer to [[RAREMETALWORKER_method | '''method''']].
