ariel-wu
commented
1 year ago Hi, Thanks for reaching out. Using ../example/200_100.pheno.plink3 there is a small issue that all the phenotypes have the same name. The option -mpheno recognizes the phenotype name (in the first row) instead of the number of columns. The output "There are 200 0 individuals" indicates that it's not reading any information for the second phenotype. In order to showcase a small number of samples, ../example/200_100.pheno.plink2 would be a better choice. In order to avoid future confusion, we will remove the 200_100.pheno.plink3 from examples, and add an option with the number of columns to make it easier. Thanks for pointing this out.
Dear developers,
as reported by another user, I am experiencing a strange output when running the example:
./SCORE -g ../example/200_100 -p ../example/200_100.pheno.plink3 -o ../example/test -noh2g -b 10 -mpheno 1,2and this is the output:
Binary phenotype: 0 Filling phenotype with mean: 0 Compute heritability: 0 Output write to destination ../example/test Analysing phenotype 1, 2 Read in 2 phenotypes There are 200 0 individuals with no missing phenotypes Total number of annotation groups: 1 num of random vectors: 10 No Covariate File Specified genotype size: 200 X 100 Total number of blocks: 2 Start reading genotype round 1/2... Reading chromosome 0 Reading chromosome 1 Reading chromosome 2 Reading chromosome 3 Reading chromosome 4 Reading chromosome 5 Reading chromosome 6 Reading chromosome 7 Reading chromosome 8 Reading chromosome 9 Reading chromosome 10 Reading chromosome 11 Reading chromosome 12 Reading chromosome 13 Reading chromosome 14 Reading chromosome 15 Reading chromosome 16 Reading chromosome 17 Reading chromosome 18 Reading chromosome 19 Reading chromosome 20 Reading chromosome 21 yKy427.64 -nan -nan -nan yy 199 -nan -nan -nan Coheritability factor estimation for phenotype: 0 , 1 lambda_g: -nan Weighted jackknife SE: -nan Unweighted jackknife SE: -nan Jack Knife SE: -nan