iplotMScanone within R Markdown

In qtlcharts: Interactive Graphics for QTL Experiments

This document serves to test the R/qtlcharts function iplotMScanone.

knitr::opts_chunk$set(fig.width=9, fig.height=6)
set.seed(69891250)
library(qtl)
library(qtlcharts)
data(grav)

Reduce size of data.

grav$pheno <- grav$pheno[,seq(1, nphe(grav), by=5)]
times <- as.numeric(sub("T", "", phenames(grav)))/60

Run scanone.

grav <- calc.genoprob(grav, step=1)
out.hk <- scanone(grav, pheno.col=1:nphe(grav), method="hk")

iplotMScanone(out.hk, grav, chartOpts=list(eff_ylab="QTL effect"))

qtlcharts documentation built on Jan. 8, 2022, 1:06 a.m.