coloc analysis still broken, even on earlier versions

[Chris-Wills]

I am running the following command:

Rscript ../../FUSION/FUSION.assoc_test.R \
        --sumstats "$sumstats" \
        --weights "$weights" \
        --weights_dir "$weights_dir" \
        --ref_ld_chr "$ref_ld_chr" \
        --chr "$i" \
        --coloc_P 0.001 \
        --PANELN "$weights" \
        --GWASN 6697 \
        --out "$out" 

When --coloc_P is removed everything runs smoothly, when it is added NA is returned for everything. I tried using coloc package versions 5.1.0.1 and 5.1.0 as suggested in previous posts but nothing has changed.

[Chris-Wills]

Rolling back all the way to coloc v3.2-1 fixed it.

[SToikumo]

Hi @Chris-Wills,

How did you roll back to coloc v3.2-1? I am having a similar issue at the moment.

I look forward to your thoughts.

[Chris-Wills]

Hi @Chris-Wills,

How did you roll back to coloc v3.2-1? I am having a similar issue at the moment.

I look forward to your thoughts.

You can download old builds of packages straight from CRAN, coloc is here

Make sure to uninstall the current build first