GWAStest: GWAS with PCA

In stp4freedom/GWhEAT: Performed GWAS in a fast and efficient manner

Description

GWAS with PCA

Usage

GWAStest(
  phenotypes = NULL,
  genotypes = NULL,
  Cov = NULL,
  GM = NULL,
  PCA.M = 3,
  QTN.position = NULL,
  cutoff = NULL
)

Arguments

phenotypes	file with numeric phenotypic values
genotypes	data.frame with genotype calls coded as 0,1,2.
Cov	numeric data.frame with covariates values
GM	genetic map of data with chr and position of each SNP
PCA.M	number of principal components to use default is 3
QTN.position	posistion of QTN if applicable
cutoff	If cutoff is default, uses Bonferroni; else uses -log(value) of 0.05/number of SNPs

Value

Manhatten plot, QQ plot plus p-values, type-1 error and power for every SNP

stp4freedom/GWhEAT documentation built on April 3, 2020, 4:21 a.m.