R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.

사용법 요약 #

데이터 로드 (genotype, phenotype 따로. genotype은 A, H, B, C, D로 코드)

library(qtl)
potato <- read.cross("csvs", ".", "potato_geno.csv", "potato_pheno.csv")
potato <- drop.nullmarkers(potato)

모든 마커들간에 Recombination fractions 계산, LOD score 계산

potato <- est.rf(potato)  
plotRF(potato)
plotRF(potato, chr=c(1,4))

Genetic map 재 추정

newmap <- est.map(potato, error.prob=0.01)  # re-estimate genetic map
potato <- replace.map(potato, newmap)

genotyping error 확인

potato <- calc.errorlod(potato, error.prob=0.01)
plotGeno(potato)
plotInfo(potato)

마지막으로, QTL mapping

potato <- calc.genoprob(potato, step=1, error.prob=0.01)
out.em <- scanone(potato)
out.hk <- scanone(potato, method="hk")
out.sim <- sim.geno(potato, step=2, n.draws=16, error.prob=0.01)
out.imp <- scanone(out.sim, method="imp")

그림확인

plot(out.em)
plot(out.em, out.hk, out.imp, chr=c(1,4,15))
plot(out.imp, col="red", add=TRUE)

Incoming Links #

Related Articles (Article 0) #

• QTL

Suggested Pages #

• 0.299 eQTL
• 0.025 SNP array
• 0.025 April 13
• 0.025 Newton Morton
• 0.025 Python
• 0.025 Homebrew
• 0.025 Programming language
• 0.025 August 29
• 0.025 OS X
• 0.025 2016
• More suggestions...