R qtl package 使用记录

 

1.  qtl安装了很多次，提示R版本不符合；重启了R，安装成功

2. 画出的图如下，更详细的linkage map 图需要借助其它软件

########################

install.packages("qtl")

library(qtl)

source("https://bioconductor.org/biocLite.R")

install.packages("BiocManager") 
BiocManager::install("qtl")
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
##########################################

data(fake.bc)
ls()
summary(fake.bc)
plot.missing(fake.bc)
fake.bc <- drop.nullmarkers(fake.bc)
totmar(fake.bc)
fake.bc <- calc.genoprob(fake.bc, step=1, error.prob=0.01)
out.em <- scanone(fake.bc)
out.hk <- scanone(fake.bc, method="hk")
fake.bc <- sim.geno(fake.bc, step=2, n.draws=16, error.prob=0.01)
out.imp <- scanone(fake.bc, method="imp")
summary(out.em)
summary(out.em, threshold = 3)
summary(out.hk, threshold = 3)
summary(out.imp, threshold = 3)

max(out.em) # based on expectation maximization

max(out.hk) # based on Haley-Knott regression

max(out.imp) # based on multiple imputation

plot(out.em, chr=c(2,5))
plot(out.em, out.hk, out.imp, chr=c(2,5))