Post by Nelson Barrientos on Dec 16, 2020 0:40:55 GMT
Hello,
I will convert my QTLtools output to BESD format soon. However, I noticed that your tool is still using the output format for the older version of QTLtools. My qtl output from permutation run has the new format where 2 extra columns are added: See below:
1 phe_id | grp_id The phenotype ID or if one of the grouping options is provided, then phenotype group ID
2 phe_chr The phenotype chromosome
3 phe_from Start position of the phenotype
4 phe_to End position of the phenotype
5 phe_strd The phenotype strand
6 n_var_in_cis The number variants in the cis window for this phenotype.
7 dist_phe_var The distance between the variant and the phenotype start positions.
8 var_id The most significant variant ID.
9 var_chr The most significant variant's chromosome.
10 var_from The start position of the most significant variant.
11 var_to The end position of the most significant variant.
12 dof1 The number of degrees of freedom used to compute the p-values.
13 dof2 Estimated number of degrees of freedom used in beta approximation p-value calculations.
14 bml1 The first shape parameter of the fitted beta distribution (alpha parameter). These should be close to 1.
15 bml2 The second shape parameter of the fitted beta distribution (beta parameter). This corresponds to the effective number of independent tests in the region.
16 nom_pval The nominal p-value of the association between the most significant variant and the phenotype.
17 r_squared The r squared of the linear regression.
18 slope The beta (slope) of the linear regression.
18.1 slope_se The standard error of the beta. Only printed if --std-err is provided.
19 adj_emp_pval Adjusted empirical p-value from permutations. This is the adjusted p-value not using the beta approximation. Simply calculated as: (number of p-values observed during permutations that were smaller than or equal to the nominal p-value + 1) / (number of permutations + 1). The most significant p-value achievable would be 1 / (number of permutations + 1).
20 adj_beta_pval Adjusted empirical p-value given by the fitted beta distribution. We strongly recommend using this adjusted p-value in any downstream analysis.
I was wondering if the fact that my file has column 17 (r_squared) and 18.1 (SE of beta) will affect when I attempt to make the BESD file.
Thank you so much for this tool and thank you beforehand for your help.
Nelson
I will convert my QTLtools output to BESD format soon. However, I noticed that your tool is still using the output format for the older version of QTLtools. My qtl output from permutation run has the new format where 2 extra columns are added: See below:
1 phe_id | grp_id The phenotype ID or if one of the grouping options is provided, then phenotype group ID
2 phe_chr The phenotype chromosome
3 phe_from Start position of the phenotype
4 phe_to End position of the phenotype
5 phe_strd The phenotype strand
6 n_var_in_cis The number variants in the cis window for this phenotype.
7 dist_phe_var The distance between the variant and the phenotype start positions.
8 var_id The most significant variant ID.
9 var_chr The most significant variant's chromosome.
10 var_from The start position of the most significant variant.
11 var_to The end position of the most significant variant.
12 dof1 The number of degrees of freedom used to compute the p-values.
13 dof2 Estimated number of degrees of freedom used in beta approximation p-value calculations.
14 bml1 The first shape parameter of the fitted beta distribution (alpha parameter). These should be close to 1.
15 bml2 The second shape parameter of the fitted beta distribution (beta parameter). This corresponds to the effective number of independent tests in the region.
16 nom_pval The nominal p-value of the association between the most significant variant and the phenotype.
17 r_squared The r squared of the linear regression.
18 slope The beta (slope) of the linear regression.
18.1 slope_se The standard error of the beta. Only printed if --std-err is provided.
19 adj_emp_pval Adjusted empirical p-value from permutations. This is the adjusted p-value not using the beta approximation. Simply calculated as: (number of p-values observed during permutations that were smaller than or equal to the nominal p-value + 1) / (number of permutations + 1). The most significant p-value achievable would be 1 / (number of permutations + 1).
20 adj_beta_pval Adjusted empirical p-value given by the fitted beta distribution. We strongly recommend using this adjusted p-value in any downstream analysis.
I was wondering if the fact that my file has column 17 (r_squared) and 18.1 (SE of beta) will affect when I attempt to make the BESD file.
Thank you so much for this tool and thank you beforehand for your help.
Nelson