densityPlot function

Plot profile likelihood density for a single SNP.

This function plots the density distribution for a single SNP calculated from the evian functions.

densityPlot(dList, snpName, kcut = NULL, pl = 'linear', xlim = NULL,
  color = c('red','orange','green','blue'), round = 2,legend_cex=1)

Arguments

• dList: a row-combined list, output from evian.
• snpName: a string specifying the SNP to be plotted.
• kcut: numeric; the cut-off to be plotted. If kcut=NULL, all values of k in the kcutoff will be plotted.
• pl: a string specifying the y-axis for the plot. The y-axis will be plotted as 'Odds Ratio' if pl is specified as logit, 'Beta' otherwise.
• xlim: graphical parameter used in plot function
• color: 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.
• round: numeric; number of digits displayed on the plot.
• legend_cex: numeric; control the size of the legend, default 1.

Details

This function takes output from evian as input. It will plot the density of the estimated standardized profile likelihood for the SNP of interest. Some basic summary statistics will be included on the plot too.

References

Strug, L. J., Hodge, S. E., Chiang, T., Pal, D. K., Corey, P. N., & Rohde, C. (2010). A pure likelihood approach to the analysis of genetic association data: an alternative to Bayesian and frequentist analysis. Eur J Hum Genet, 18(8), 933-941. doi:10.1038/ejhg.2010.47

Royall, R. (1997). Statistical Evidence: A Likelihood Paradigm. London, Chapman and Hall.

Examples

data(evian_linear_raw)
data(evian_linear_bim)
rst1=evian(data=evian_linear_raw, bim=evian_linear_bim, xcols=10:ncol(evian_linear_raw),
      ycol=6, covariateCol=c(5,7:9), robust=FALSE, model="additive", m=200, lolim=-0.4,
      hilim=0.4, kcutoff = c(32,100), multiThread=1,family='gaussian',plinkCC=FALSE)

# Plot the density for rs912
densityPlot(dList=rst1,snpName='rs912')