evian (version 2.1.0)

glr_plot: Plot methods for multiple glr result in a genomic region.

Description

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

Usage

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

# NOT RUN {
  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))


# }