Adjust GWAS Z-statistic — adjust

Adjust the GWAS Z-statistic.

adjust_zstat(
  dat,
  drop_MHC = TRUE,
  method = "bonferroni",
  model = NULL,
  log_vars = c("NSNPS", "NPARAM", "GENELEN"),
  formula = ZSTAT ~ NSNPS + logNSNPS + NPARAM + logNPARAM + GENELEN + logGENELEN,
  verbose = TRUE,
  ...
)

Arguments

dat	`data.table` produced by map_snps2genes_txdb.
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.
log_vars	Variables to perform natural log transformation on first. Only run on variables available in `dat`.
formula	Formula to use in `model`.
...	Additional arguments passed to `model`.

Value

dat with the new column "ADJ_ZSTAT".

Details

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