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Computes causal SNP's

GWAS.Rd

This function is heavily build onto bigstatsr::big_univLinReg. For more documentation check
https://privefl.github.io/bigstatsr/reference/big_univLinReg.html

Usage

GWAS(G, y, p, logreg = FALSE, ncores = 1)

Arguments

G

A file backed matrix with SNP data.

y

A vector containing targets for each position.

p

The significance level.

logreg

If TRUE do logistic regression, else Linear regression.

ncores

Amount of cores to use.

Value

A matrix containing:

  • The slopes of each regression

  • The standard errors of each slope

  • If logreg = T: the number of iterations for each slope. If NA, it means that the algorithm didn't converge, and glm was used instead.

  • The t-scores associated with each slope.

  • The p-values for each slope

  • And a binary vector saying if the position is causal or not given p