multiLine_plot: Plot methods for multiple likelihood intervals in a genomic...
In evian: Evidential Analysis of Genetic Association Data

Description Usage Arguments Details Author(s) References Examples

This function plots the likelihood intervals (LIs) for all SNPs calculated using evian .

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  multiLine_plot(bpstart = 0, bpend = 1000000000, dList, title = NULL,
  showmaxlr = 3, kcut = NULL, pl = 'linear', ylim = c(-0.5,10),
  color = c('violet','green','red','blue'), markSNP = NULL, round = 2,legend_cex=1)

`bpstart,bpend`	numeric; indicating the range of base pairs to be plotted. From `bpstart` to `bpend`.
`dList`	a row-combined list, output from `evian`.
`title`	string; title of plot
`showmaxlr`	numeric; number of top SNPs to display on the graph. Default = 3. SNPs are chosen by their maximum likelihood ratio values.
`kcut`	numeric; the cut-off to be plotted. If `kcut`=`NULL`, all intervals 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.
`markSNP`	vector of strings; indicates which SNPs to be marked on the plot. By default it will mark all SNPs that are significant at the smallest cut-off.
`round`	numeric; number of digits displayed on the plot.
`ylim`	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.
`legend_cex`	numeric; control the size of the legend, default 1.

This function takes output from evian as input. It will plot the likelihood intervals for each of the SNPs analyzed. If 1/k interval is significant then it will be colored by the specified color and will remain grey if the interval is not significant.

Dr. Lisa J Strug lisa.strug@utoronto.ca

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

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 LIs for all 3 SNPs
multiLine_plot(dList=rst1)