hakyimlab/brainxcan

brainxcan's Issues

installation of R packages

HI there,
Some R packages, such as 'rgeos,' 'oro.nifti,' and 'raster,' are hard to install on R. Is there a workaround for this?

Error in MR

I have been using BrainXcan for a project and have recently run into an issue with getting one particular set of MR results. When running, I get the error:

Failed to open local file '~/BrainXcan/brainxcan_data/idp_gwas/residual.t1_PC-Subcortical.chr1/GMvol-1.parquet'

When I look at the downloaded brainxcan_data files (from the Zenodo directory), in the idp_gwas folder I see that instead of having a separate folder called residual.t1_PC-Subcortical.chr[num], those files are simply within each of my residual.t1 folders. For instance, within residual.t1.chr1, I see a file PC-Subcortical_GMvol-1.parquet, which is what I'm assuming the program needs to run properly. I'm not sure why the code is directing to an incorrect folder here or how to fix this issue. I'd appreciate any help with this!

verison of R?

Hi! What version of R did you guys use to write the snakemake scripts? I keep getting weird dependency issues for packages that don't seem to install on some versions of R (ie rgeos, rgdal) when I run the snakemake script. Thanks!