Create a gwas_data object

Convert a data.frame to the standardized gwas_data format used by all ggwas plotting functions.

Usage

as_gwas_data(
  x,
  chr = NULL,
  bp = NULL,
  snp = NULL,
  p = NULL,
  beta = NULL,
  se = NULL,
  a1 = NULL,
  a2 = NULL,
  af = NULL,
  n = NULL,
  info = NULL,
  log_p = FALSE
)

Arguments

x

A data.frame, tibble, data.table, or a Bioconductor GRanges object (variant positions are taken from the ranges and association statistics from the metadata columns).

chr, bp, snp, p, beta, se, a1, a2, af, n, info

Column names to use. If NULL, auto-detection is attempted.

log_p

If TRUE, the p-value column contains -log10(p) values that will be back-transformed.

Value

A tibble with class gwas_data.

Examples

df <- data.frame(CHR = c(1, 1, 2), BP = c(1e6, 2e6, 5e6),
                 P = c(1e-8, 0.5, 0.01), SNP = c("rs1", "rs2", "rs3"))
gd <- as_gwas_data(df)
gd
#> A gwas_data object: 3 variants across 2 chromosomes
#>   Min p-value: 1.00e-08
#>   Lambda GC:   14.584
#>   Columns:     CHR, BP, SNP, P