GWASapply: GWAS with PCA

In stp4freedom/HW4_GLM_GWAS: Genome Wide Efficient Association Test (GWhEAT)

Description

GWAS with PCA

Usage

GWASapply(
  pheno = NULL,
  geno = NULL,
  Cov = NULL,
  GM = NULL,
  PCA.M = 3,
  QTN.position = NULL,
  cutoff = NULL,
  plots = FALSE,
  messages = FALSE,
  print = FALSE,
  trait = "unknown"
)

Arguments

pheno	file with numeric phenotypic values
geno	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
plots	if TRUE, function plots PCA graphs, Manhatten Plot and QQ plot
messages	if TRUE, returns messages for the GWAS function
print	if TRUE, results are saved in a CSV
trait	character value for trait name

Value

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

stp4freedom/HW4_GLM_GWAS documentation built on March 29, 2020, 6:49 p.m.