cpg: Methods for object of class `"cpg"`

Description

Methods and extra functions for class "cpg". plot.cpg creates a QQ plot based on the association p-values or t-statistics from the function cpg.assoc.

Usage

# S3 method for cpg
plot(x, save.plot = NULL, file.type = "pdf", popup.pdf = FALSE, 
                     tplot = FALSE, classic = TRUE,main.title = NULL, eps.size = c(5, 5),
                     gc.p.val = FALSE, gcdisplay = FALSE, ...)
  # S3 method for cpg
summary(object,...)
  # S3 method for cpg
print(x,...)
  # S3 method for cpg
sort(x,decreasing,...)

Value

sort.cpg returns an item of class "cpg" that is sorted by p-value. summary.cpg creates a qq-plot based on the data, and scatterplots or boxplots for the top sites.

Arguments

x: Output of class "cpg" from cpg.assoc or cpg.work.
save.plot: Name of the file for the plot to be saved to. If not specified, plot will not be saved.
file.type: Type of file to be saved. Can either be "pdf" or "eps". Selecting file.type="eps" will result in publication quality editable postscript files that can be opened by Adobe Illustrator or Photoshop.
popup.pdf: TRUE or FALSE. If creating a pdf file, this indicates if the plot should appear in a popup window as well. If running in a cluster-like environment, best to leave FALSE.
tplot: Logical. If TRUE, t-statistics will be plotted vs. their expected quantiles. If FALSE (default), -log(p) will be plotted. (Note: if class(x$indep)=='factor' this option will be ignored.)
classic: Logical. If TRUE, a classic qq-plot will be generated, with all p-values plotted against predicted values (including significant). If FALSE Holm-significant CpG sites will not be used to compute expected quantiles and will be plotted separately.
main.title: Main title to be put on the graph. If NULL one based on the analysis will be used.
eps.size: Vector indicating the size of .eps file (if creating one). Corresponds to the options horizontal and height in the postscript function.
gc.p.val: Logical. If true, plot will use the genomic control adjusted p-values.
gcdisplay: Logical.If true, plot will display the genomic control value in the legend.
object: Output of class "cpg" from cpg.assoc or cpg.work.
decreasing: logical. Should the sort be increasing or decreasing? Not available for partial sorting.
...: Arguments to be passed to methods, such as graphical parameters.

Author

Barfield, R.; Kilaru,V.; Conneely, K.
Maintainer: R. Barfield: <barfieldrichard8@gmail.com>

Examples

Run this code

##QQ Plot:
data(samplecpg,samplepheno,package="CpGassoc")
test<-cpg.assoc(samplecpg,samplepheno$weight,large.data=FALSE)
plot(test)
##t-statistic plot:
plot(test,tplot=TRUE)


#Getting our plot:
plot(test,classic=FALSE)


##Now an example of sort
head(sort(test)$results)

##Summary
summary(test)