plotQTL: Make a plot of QTL mapping result

In venyao/binQTL: QTL mapping with binmap

Description

The qtl.res data frame should contain 5 columns. Each row of this data frame represents a QTL. The 1st column is the ID of a Bin representing a QTL. The 2nd column is the chromosome ID of each QTL. The 3rd column is the start coordinate of a QTL. The 4th column is the end coordinate of a QTL. The 5th column is the negative Log P value of QTL scanning.

Usage

   plotQTL(qtl.res="", y.bottom=0, y.top=2, cols=c("grey30", "grey70"),
           ylab="-logp", xlab="", ...)

Arguments

qtl.res	A data frame of QTL scanning result.
y.bottom	A numeric number indicating the min y coordinate range.
y.top	A numeric number used to alter the max y coordinate range.
cols	Colours used to indicate different chromosome.
ylab	Y axis label.
xlab	X axis label.
...	parameters passed to plot.

Author(s)

Wen Yao

Examples

 
  ril.phe <- read.csv(system.file("examples/ril.phe.csv", package="binQTL"), as.is=TRUE)
  dim(ril.phe)
  ril.geno <- read.csv(system.file("examples/ril.geno.csv", package="binQTL"), as.is=TRUE)
  dim(ril.geno)
  qtl.res <- aovQTL(phenotype = ril.phe, genotype = ril.geno)
  plotQTL(qtl.res[, c(1:4, 6)], main="ANOVA", cex.axis=0.6, ylab=expression(-log[10](p)))
 

venyao/binQTL documentation built on June 9, 2019, 4:52 a.m.