manhattan function

Creating a manhattan plot

Creating a manhattan plot

This function was designed to create a manhattan plot using a data frame with columns "Chrom" (Chromosome), "Position" and "p.val" (significance for the test).

manhattan(map, col=NULL, fdr.level=0.05, show.fdr=TRUE, PVCN=NULL, ylim=NULL, ...)

Arguments

  • map: the data frame with 3 columns with names; "Chrom" (Chromosome), "Position" and "p.val" (significance for the test).
  • col: colors prefered by the user to be used in the manhattan plot. The default is NULL which will use the red-blue palette.
  • fdr.level: false discovery rate to be drawn in the plot.
  • show.fdr: a TRUE/FALSE value indicating if the FDR value should be shown in the manhattan plot or not. By default is TRUE meaning that will be displayed.
  • PVCN: In case the user wants to provide the name of the column that should be treated as the "p.val" column expected by the program in the 'map' argument.
  • ylim: the y axis limits for the manhattan plot if the user wants to customize it. By default the plot will reflect the minimum and maximum values found.
  • ...: additional arguments to be passed to the plot function such as pch, cex, etc.

Returns

If all parameters are correctly indicated the program will return:

  • $plot.data: a manhattan plot

References

Covarrubias-Pazaran G (2016) Genome assisted prediction of quantitative traits using the R package sommer. PLoS ONE 11(6): doi:10.1371/journal.pone.0156744

Author(s)

Giovanny Covarrubias-Pazaran

Examples

#random population of 200 lines with 1000 markers M <- matrix(rep(0,200*1000),1000,200) for (i in 1:200) { M[,i] <- ifelse(runif(1000)<0.5,-1,1) } colnames(M) <- 1:200 set.seed(1234) pp <- abs(rnorm(500,0,3));pp[23:34] <- abs(rnorm(12,0,20)) geno <- data.frame(Locus=paste("m",1:500, sep="."),Chrom=sort(rep(c(1:5),100)), Position=rep(seq(1,100,1),5), p.val=pp, check.names=FALSE) geno$Locus <- as.character(geno$Locus) ## look at the data, 5LGs, 100 markers in each ## -log(p.val) value for simulated trait head(geno) tail(geno) manhattan(geno)

See Also

The core functions of the package mmer

  • Maintainer: Giovanny Covarrubias-Pazaran
  • License: GPL (>= 2)
  • Last published: 2024-10-20