manhattan: manhattan plot

In Caleb-Huo/genomicLibrary: commonly used genomic functions in R

Description

manhattan plot

Usage

manhattan(dataframe, maxy = NULL, suggestiveline = 0,
  genomewideline = -log10(5e-08), axisSize = 20, labelSize = 5,
  annotate = F, SNPlogic = NULL)

Arguments

dataframe,	same as qqman package, 4 columns including SNP, CHR, BP and P
maxy	maximum of y axis
suggestiveline	0
genomewideline	default -log10(5e-8)
axisSize	default 20
labelSize	default 5
annotate	F
SNPlogic	which SNP need to be annotated in the plot
title	title

Details

manhattan plot. Input a dataframe including CHR, BP, P, SNP

Author(s)

Caleb

Examples

gwasResults1 <- data.frame(SNP=paste0("rs1",1:40), CHR=1, BP = 1:400, P=runif(400))
gwasResults2 <- data.frame(SNP=paste0("rs2",1:40), CHR=2, BP = 1:600, P=runif(600))
gwasResults <- rbind(gwasResults1, gwasResults2)
manhattan(gwasResults)
manhattan(gwasResults, annotate=T, SNPlogic=c(100,200,300,310))

Caleb-Huo/genomicLibrary documentation built on June 4, 2020, 3:54 a.m.