multiLine_plot function

Plot methods for multiple likelihood intervals in a genomic region.

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

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)

Arguments

• 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.

Details

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.

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

Author(s)

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

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 LIs for all 3 SNPs
multiLine_plot(dList=rst1)