glr_plot function

Plot methods for multiple glr result in a genomic region.

This function plots the log10 GLR value in the region calculated from the glr functions.

glr_plot(glr, snpName,kcut,col,legend_cex=1,...)

Arguments

• glr: a dataframe, output from glr.
• snpName: a string specifying the SNP to be marked.
• kcut: numeric; the cut-off to be plotted. Can have value <=1.
• col: color of the likelihood interval lines from smallest to largest. For instance, c('red','green') for LIs of k=c(8,32) means that the 1/8 interval will be plotted as red, and 1/32 will be plotted as green.
• legend_cex: numeric; control the size of the legend, default 1.
• ...: Argument passed to the plot function.

Details

This function takes output from glr as input. It will plot the GLR value on a log-scale and marked the SNPs of interests (defaultly the SNP with the maximum GLR values).

Examples

data(evian_linear_raw)
  data(evian_linear_bim)
  rst2=glr(data=evian_linear_raw, bim=evian_linear_bim, xcols=10:ncol(evian_linear_raw),
             ycol=6, covariateCol=c(5,7:9), c=0.025,robust=F, model="additive",
             m=200, lolim=-0.6, hilim=0.6, multiThread=1,family='gaussian',plinkCC=FALSE)

  # Plot the density for rs912
  glr_plot(glr=rst2,ylim=c(-0.5,2))