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Compute the genomic inflation factor (lambda GC)

Source: R/utils.R
lambda_gc.Rd

Calculates lambda GC as the ratio of the median observed chi-squared statistic (derived from p-values) to the expected median under the null (0.4549). A value near 1.0 indicates no inflation; values above ~1.05 suggest population stratification or other confounding.

Usage

lambda_gc(x, ...)

# S3 method for class 'numeric'
lambda_gc(x, ...)

# S3 method for class 'data.frame'
lambda_gc(x, ...)

# S3 method for class 'GWASFormatter'
lambda_gc(x, ...)

Arguments

x

A numeric vector of p-values, a data.frame/tibble with a `PVALUE` column, or a GWASFormatter object.

...

Additional arguments (unused).

Value

A single numeric value: the genomic inflation factor.

Methods (by class)

  • lambda_gc(numeric): Method for numeric vectors of p-values

  • lambda_gc(data.frame): Method for data.frame/tibble with a PVALUE column

  • lambda_gc(GWASFormatter): Method for GWASFormatter objects