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Al-Murphy / MungeSumstats

Rapid standardisation and quality control of GWAS or QTL summary statistics
https://doi.org/doi:10.18129/B9.bioc.MungeSumstats
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Add function to infer MAF #2

Closed Al-Murphy closed 3 years ago

Al-Murphy commented 3 years ago

May be useful to infer MAF although the downside is this wouldn't be related to the population in question so could result in questionable results. Similar code is here, taking MAF from UK Biobank: https://github.com/RajLabMSSM/echolocatoR/blob/dev/R/UKBiobank_LD.R function located here: https://github.com/RajLabMSSM/echolocatoR/blob/6b9086d6755be0cc802027b76fb8314058fa0bf1/R/standardize.R#L304

bschilder commented 3 years ago

After discussing this with @Al-Murphy, we've decided it's beyond the scope of MungeSumstats to handle this. Inferring the right population/subpopulation is a very case-by-case task and will depend on the objectives of the user. Ideally, MAF should be inferred from the same sample that the GWAS was conducted in, but this information if not always possible to obtain, further complicating this situation.