search

n-mounier / MRlap

R package to perform two-sample Mendelian Randomisation (MR) analyses using (potentially) overlapping samples
GNU General Public License v2.0
50 stars 11 forks source link

Weights for the Aisan population #11

Open jacob-mei opened 10 months ago

jacob-mei commented 10 months ago

"Expects LD scores formated as required by the original LD score regression software. Weights for the european population can be obtained by downloading the eur_w_ld_chr folder in the link below (Note that these are the same weights provided by the original developers of LDSC)“

may I ask when it comes to Aisan population, where to find the Weights for the Aisan population

lcpilling commented 10 months ago

LD Scores for EAS population were made available by the Alkes group alongisde the EUR data (https://doi.org/10.5281/zenodo.7768714).

Another option for LD Scores are those from the "Pan UK Biobank" team. See https://pan.ukbb.broadinstitute.org/blog/2020/10/29/ld-release/index.html. This includes the following genetic ancestries (using their terminology): African (AFR), Admixed American (AMR), Central/South Asian (CSA), East Asian (EAS), non-Finnish European (EUR), and Middle Eastern (MID). Though with the caveat of course, that these people are living in the UK so will not necessarily reflect the genetic diversity if whatever sample you are analyzing.

jacob-mei commented 10 months ago

Thanks for answering! helped.

jacob-mei commented 10 months ago

"hm3: This file can be obtained from https://utexas.box.com/s/vkd36n197m8klbaio3yzoxsee6sxo11v.d"

may I ask where to find this hm3 SNPlist file for Asian, I have tried to search but I don't think I have found the right one. so desperated looking for the help

lcpilling commented 10 months ago

The Alkes group have posted the data to Zenodo https://doi.org/10.5281/zenodo.7768714