I'm unable to pass my precalculated phenotype variant estimates:
> pwcoco-master/build/pwcoco \
--bfile plinkout \
--sum_stats1 exposure \
--sum_stats2 outcome \
--pve1 0.5 \
--pve2 0.4 \
--out output \
--log log \
--verbose
[...]
[2023-11-21 16:59:17.967] [info] --pve1 0.0.
[2023-11-21 16:59:17.967] [info] --pve2 0.0.
[...]
[2023-11-21 16:59:17.967] [pwcoco_log] [info] Reading data from phenotype file: exposure.
[2023-11-21 16:59:17.968] [pwcoco_log] [warning] It is preferable to use the full summary statistics to estimate the phenotype variance; you can ignore this warning if the summary statistics file you have provided are the full summary statistics.
[2023-11-21 16:59:17.968] [pwcoco_log] [warning] You can calculate the full phenotype variance by using either the '--pve' flag or '--pve_file' flag.
[2023-11-21 16:59:17.999] [pwcoco_log] [info] Read a total of: 5516 lines in phenotype file exposure.
[2023-11-21 16:59:17.999] [pwcoco_log] [info] Phenotypic variance estimated from summary statistcs of all SNPs: 0.48
[2023-11-21 16:59:17.999] [pwcoco_log] [info] Reading data from phenotype file: outcome.
[2023-11-21 16:59:17.999] [pwcoco_log] [warning] It is preferable to use the full summary statistics to estimate the phenotype variance; you can ignore this warning if the summary statistics file you have provided are the full summary statistics.
[2023-11-21 16:59:17.999] [pwcoco_log] [warning] You can calculate the full phenotype variance by using either the '--pve' flag or '--pve_file' flag.
[2023-11-21 16:59:18.003] [pwcoco_log] [info] Read a total of: 717 lines in phenotype file outcome.
[2023-11-21 16:59:18.003] [pwcoco_log] [info] Phenotypic variance estimated from summary statistcs of all SNPs: 0.29
I also tried passing them as a string (--pve1 "0.5" for example), again no luck. The implementation seems to round it down to the next integer, as 1.4 is rounded to 1.0
Hi!
I'm unable to pass my precalculated phenotype variant estimates:
I also tried passing them as a string (--pve1 "0.5" for example), again no luck. The implementation seems to round it down to the next integer, as 1.4 is rounded to 1.0