Incomplete provided reference panels for subsampling

[rmandla]

Hi,

I'm interested in subsampling my GWAS using your script, but it seems to require LD data that is not provided in box.

I downloaded all the LD data from the provided box link (https://uwmadison.app.box.com/s/6yv7u8wxm6zutj7763jekdhed47kl0f1), which contains the 1kg.RData and 1kg_hm3_QCed_noM.* files. However, the subsampling script requires two RData files, ld_1kg.RData and rs_1kg.RData, which are not in the box link.

Does the 1kg.RData in box correspond to the ld_1kg.RData file or the rs_1kg.RData file? And where can I download the missing RData file?

Thanks,

Ravi

[rmandla]

Looks like the issue is actually in the PUMAS.subsampling.R script. To solve it, these lines:

    load(paste0(ld_path, "/ld_1kg.RData"))
    load(paste0(ld_path, "/rs_1kg.RData"))

should be replaced with

load(ld_path)