densityPlot: Plot profile likelihood density for a single SNP.
In evian: Evidential Analysis of Genetic Association Data

Description Usage Arguments Details References Examples

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

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

`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.

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.

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.

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')