snp.effects.plot: Effects plot

Description Usage Arguments Details See Also Examples

View source: R/wga_plot.R

Description

Creates a plot of the effects returned from snp.effects

Usage

1
 snp.effects.plot(obj.list, op=NULL)

Arguments

obj.list

Return object or list of return objects from snp.effects. No default.

op

List of options (see details). The default is NULL.

Details

Plots the effects returned from snp.effects. By default, the effects in StratEffects for each method will be plotted. The side of the effect will have a sawtooth edge if the effect goes beyond the limits of the plot.

Options list op: Below are the names for the options list op. All names have default values if they are not specified.

See Also

snp.effects

Examples

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 # Use the ovarian cancer data
 data(Xdata, package="CGEN")

 # Add some fake SNPs
 set.seed(636)
 Xdata[, "rs123"] <- rbinom(nrow(Xdata), 1, 0.4)
 Xdata[, "rs456"] <- rbinom(nrow(Xdata), 1, 0.4)
 Xdata[, "rs789"] <- rbinom(nrow(Xdata), 1, 0.4)

 snpVars <- c("BRCA.status", "rs123", "rs456", "rs789")
 objects <- list()
 for (i in 1:length(snpVars)) {
   fit <- snp.logistic(Xdata, "case.control", snpVars[i],
                     main.vars=c("oral.years", "n.children"), 
                     int.vars=c("oral.years", "n.children"), 
                     strata.var="ethnic.group")

   # Compute the effects
   objects[[i]] <- snp.effects(fit, "oral.years", var.levels=0:4)
 } 

 # Plot
 snp.effects.plot(objects)

 # Plot all on the same scale
 #snp.effects.plot(objects, op=list(ylim=c(0.9, 1.4), legend=list(x="bottom")))

 # Plot all the joint effects of rs789 for the CML method and add confidence intervals
 #snp.effects.plot(objects[[4]], op=list(method="CML", type="JointEffects",
 #        legend=list(x="bottomleft", inset=0), ylim=c(0.45, 1.3),
 #        colors=c("blue", "aquamarine", "skyblue"), addCI=1))

CGEN documentation built on May 31, 2017, 2:24 p.m.

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