Post by aniek on Oct 20, 2016 15:31:04 GMT
Hello,
How does GCTA --reml treat repeated records on individuals? I have a phenotype file with 3524 records from 2319 individuals that are included in my GRM. Does it take only the first record per individual (and have a diagonal design matrix for the breeding values) or use all records of an animal to estimate the breeding values (and have a design matrix with records in the rows and individuals in the columns and a 1 for each record from the individual)? From the output below it seems that only 2319 records are used for the reml analysis.
If GCTA can handle repeated records would it then also be possible to estimate a permanent environment effect and how and would that also be true for the mlma analysis?
Many thanks for any help,
Aniek
Part of my GCTA output regarding reml analysis feeding repeated records on 2319 individuals (./gcta64 --reml --grm geno85k --pheno CLA.phen --reml-pred-rand --out repeated):
Reading IDs of the GRM from [geno85k.grm.id].
2447 IDs read from [geno85k.grm.id].
Reading the GRM from [geno85k.grm.bin].
Reading the number of SNPs for the GRM from [geno85k.grm.N.bin].
Pairwise genetic relationships between 2447 individuals are included from [geno85k.grm.bin].
Reading phenotypes from [CLA.phen].
Non-missing phenotypes of 3524 individuals are included from [CLA.phen].
2319 individuals are in common in these files.
Performing REML analysis ... (Note: may take hours depending on sample size).
2319 observations, 1 fixed effect(s), and 2 variance component(s)(including residual variance).
How does GCTA --reml treat repeated records on individuals? I have a phenotype file with 3524 records from 2319 individuals that are included in my GRM. Does it take only the first record per individual (and have a diagonal design matrix for the breeding values) or use all records of an animal to estimate the breeding values (and have a design matrix with records in the rows and individuals in the columns and a 1 for each record from the individual)? From the output below it seems that only 2319 records are used for the reml analysis.
If GCTA can handle repeated records would it then also be possible to estimate a permanent environment effect and how and would that also be true for the mlma analysis?
Many thanks for any help,
Aniek
Part of my GCTA output regarding reml analysis feeding repeated records on 2319 individuals (./gcta64 --reml --grm geno85k --pheno CLA.phen --reml-pred-rand --out repeated):
Reading IDs of the GRM from [geno85k.grm.id].
2447 IDs read from [geno85k.grm.id].
Reading the GRM from [geno85k.grm.bin].
Reading the number of SNPs for the GRM from [geno85k.grm.N.bin].
Pairwise genetic relationships between 2447 individuals are included from [geno85k.grm.bin].
Reading phenotypes from [CLA.phen].
Non-missing phenotypes of 3524 individuals are included from [CLA.phen].
2319 individuals are in common in these files.
Performing REML analysis ... (Note: may take hours depending on sample size).
2319 observations, 1 fixed effect(s), and 2 variance component(s)(including residual variance).
