Adjust GWAS Z-statistic: MAGMA

Source: R/adjust_zstat_magma.R

Adjust MAGMA Z-statistic from .genes.out files

adjust_zstat_magma(
  magma,
  drop_MHC = TRUE,
  method = "bonferroni",
  model = NULL,
  formula = ZSTAT ~ NSNPS + logNSNPS + NPARAM + logNPARAM + GENELEN + logGENELEN,
  verbose = TRUE,
  ...
)

Arguments

magma

MAGMA .genes.out data.table produced by map.snps.to.genes.
drop_MHC

Drop genes from the MHC (Major Histocompatibility Complex) region.
method

correction method, a character string. Can be abbreviated.
model

Statistical model to use. Defaults to lm.
formula

Formula to use in model.
...

Additional arguments passed to model.

Details

Used when you want to directly analyse the gene-level Z-scores corrected for gene length, etc.