manhattan_plot: Function to create a manhattan plot

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

Description

Function to create a manhattan plot

Usage

manhattan_plot(
  GM,
  pvals,
  cutoff = NULL,
  QTN_index = c(),
  FP = NULL,
  TP = NULL,
  trait = "unknown",
  messages = FALSE
)

Arguments

GM	genetic map of data with chr and position of each SNP
pvals	pvals from gwas results for each SNP
cutoff	If cutoff is default, uses Bonferroni; 0.05/number of SNPs
QTN_index	posistion of QTN if applicable
FP	Positions of SNPS that are False positives
TP	Positions of SNPS that are True positives
trait	character value for trait name
messages	if TRUE, returns messages for the GWAS function

Value

Manhatten plot

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