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

In evian: Evidential Analysis of Genetic Association Data

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

  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))

evian documentation built on May 23, 2019, 5:02 p.m.