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Perform DENTIST on a single window

Source: R/sumstatsQc.R
dentistSingleWindow.Rd

Detect outliers in GWAS summary statistics using LD-based iterative imputation. Provide either an LD correlation matrix R or a genotype matrix X (from which LD and sample size are derived automatically).

Usage

dentistSingleWindow(
  zScore,
  R = NULL,
  X = NULL,
  nSample = NULL,
  pValueThreshold = 5e-08,
  propSVD = 0.4,
  gcControl = FALSE,
  nIter = 10,
  gPvalueThreshold = 0.05,
  duprThreshold = 0.99,
  ncpus = 1,
  correctChenEtAlBug = TRUE,
  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(X) and nSample defaults to nrow(X).

nSample

Number of samples in the LD reference panel (NOT the GWAS sample size). Controls the SVD truncation rank. Required when R is provided; inferred from X when X is provided.

pValueThreshold

P-value threshold for outlier detection. Default is 5e-8.

propSVD

SVD truncation proportion. Default is 0.4.

gcControl

Logical; apply genomic control. Default is FALSE.

nIter

Number of iterations. Default is 10.

gPvalueThreshold

Grouping p-value threshold. Default is 0.05.

duprThreshold

Duplicate r-squared threshold. Default is 0.99.

ncpus

Number of CPU cores. Default is 1.

correctChenEtAlBug

Correct the original DENTIST operator! bug. Default is TRUE.

ldMethod

Character string specifying the LD computation method when X is provided. Passed to computeLd. One of "sample" (default), "population", or "gcta". Ignored when R is provided directly.

Value

Data frame with columns: original_z, imputed_z, iter_to_correct, rsq, is_duplicate, outlier_stat, outlier.

References

https://github.com/Yves-CHEN/DENTIST

See also

dentist, slalom