GWAS: Computes causal SNP's

In Holdols/genstats: Analyse genetic data

Computes causal SNP's

Description

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

Holdols/genstats documentation built on June 10, 2022, 6:05 a.m.