evian (version 2.1.0)

multiLine_plot: Plot methods for multiple likelihood intervals in a genomic region.

Description

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

Usage

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

Examples

# NOT RUN {
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)


# }