Prepare data for MR-mega approach and environment-adjusted MR-MEGA approach (mr-mega)

MR_mega_prep(
  sum_stat_pop,
  n_cohort = NULL,
  usefor = "mr-mega",
  qt = TRUE,
  pcCount = 2,
  calpc = FALSE,
  envCount = NULL,
  ncores
)

Arguments

sum_stat_pop: A list of all GWAS file data.
n_cohort: The number of the cohorts.
usefor: "mr-mega" or "env-mr-mega". The default option is "mr-mega".
qt: Whether the trait is quantitative or not. This method is only used for quantitative traits.
pcCount: The number of axes of genetic variation. Default the number of PCs is 1. The limitation of pcCount should be pcCount+envCount<n_cohort-2 for env-adjusted MR MEGA approach and The limitation of pcCount should be pcCount<n_cohort-2 for MR MEGA approach.
calpc: Logical. whether need to calculate PCs based on the inputted GWAS data.
envCount: The number of environment covariates. Default the number of environment covariates is null.The limitation of envCount should be pcCount+envCount<n_cohort-2 for env-adjusted MR MEGA approach.
ncores: The the number of cores which would be used for running in parallel.

A list containing BETA, inverse of squared SE, PCs if required, marker information, cohort_count_filt and filtered-out genetic variants.

Siru Wang