Detect LD-Summary Statistic Mismatches

Unified wrapper for detecting outlier variants due to LD-summary statistic mismatches. Dispatches to either dentistSingleWindow or slalom based on the method argument.

Usage

ldMismatchQc(
  zScore,
  R = NULL,
  X = NULL,
  nSample = NULL,
  method = c("slalom", "dentist"),
  ldMethod = "sample",
  ...
)

Arguments

zScore: Numeric vector of z-scores.
R: Square LD correlation matrix. Provide either R or X.
X: Genotype matrix (samples x SNPs). If provided, LD is computed via computeLd and nSample defaults to nrow(X).
nSample: Number of samples in the LD reference panel. Required when R is provided and method = "dentist"; inferred from X when X is provided.
method: Character string specifying the QC method: "slalom" (default) or "dentist".
ldMethod: Character string specifying the LD computation method when X is provided. One of "sample" (default), "population", or "gcta". Ignored when R is provided directly.
...: Additional arguments passed to the underlying QC method (dentistSingleWindow or slalom).

Value

A data frame with at least a logical outlier column indicating which variants are identified as outliers. The remaining columns depend on the method used.

Usage

Arguments

Value

See also