jwr-git / pwcoco

Pair-wise conditional analysis and colocalisation
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Pre-calculated `--pve` rounded down to 0.0 #6

Closed YStrauchP4 closed 10 months ago

YStrauchP4 commented 10 months ago

Hi!

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

jwr-git commented 10 months ago

Pushed a fix -- please try again :)