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xihaoli / MetaSTAAR

An R package for performing MetaSTAAR procedure in whole-genome sequencing studies
GNU General Public License v3.0
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Using summary statistics only #3

Closed oalavijeh closed 1 year ago

oalavijeh commented 1 year ago

Dear MetaSTAAR team,

Apologies for the basic question but I was wondering if metaSTAAR would work with only summary statistics and no individual level data. I have summary stats from a SAIGE-GENE analysis in two cohort at both a gene and variant level but I do not have access to covariates or individual level patient data. Is there a way to get this to work with metaSTAAR as I all the inputs seem to require a covaraite file?

Many thanks

xihaoli commented 1 year ago

Hi @oalavijeh,

Thanks for your question. MetaSTAAR is designed to work with only summary statistics and no individual-level data. Here, the summary statistics include the covariance (LD) matrices of variants in the given variant set (e.g. a gene or a region), in addition to the variant-level marginal test statistics.

Please feel free to send us via email if you would like to elaborate more. We can take a closer look and discuss this in more detail.

Best, Xihao