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Perform meta-analysis of GWAS summary statistics datasets cleaned by tidyGWAS

meta_analyze.Rd

meta_analyze() will:

  • flip the effect allele to the reference allele (using either GRCh37 or GRCh38), control with ref

  • variant id is constructed using by columns

  • EAF (allele frequency) and INFO (imputation quality) are weighted by sample size, if present

  • CaseN, N, ControlN and EffectiveN are all summed and carried forward

Usage

meta_analyze(
  dset,
  by = c("CHR", "POS", "RSID", "EffectAllele", "OtherAllele"),
  method = c("ivw"),
  ref = c("REF_37", "REF_38")
)

Arguments

dset

an arrow::open_dataset() object

by

a character vector of column names to group by. Default is c("CHR", "POS", "RSID", "EffectAllele", "OtherAllele")

method

method to use for performing meta-analysis. Currently, only IVW (based on standard errors) is supported.

ref

either "REF_37" or "REF_38", depending on which column you want to use to standardize reference allele

Value

a dplyr::tibble()

Examples

if (FALSE) { # \dontrun{
dset <- arrow::open_dataset("path_to/sumstats/")
res <- meta_analyze(dset)
} # }