manhattan_plot: Function to create a manhattan plot

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

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; else uses -log(value) of 0.05/number of SNPs
QTN_index	posistion of QTN if applicable
FP	Positions of SNPS that are False positive
TP	Positions of SNPS that are True positive
trait	character value for trait name

Value

Manhatten plot

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