Class cpg.perm {CpGassoc}  R Documentation 
"cpg.perm"
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Methods and extra functions for class "cpg.perm"
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plot.cpg.perm
creates a QQ plot based on the association pvalues or tstatistics from the function cpg.perm
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## S3 method for class 'cpg.perm' plot(x, save.plot = NULL, file.type = "pdf", popup.pdf = FALSE, main.title = NULL, eps.size = c(5, 5), tplot = FALSE, perm.ci = TRUE, classic = TRUE, gc.p.val = FALSE, gcdisplay = FALSE, ...) ## S3 method for class 'cpg.perm' summary(object,...) ## S3 method for class 'cpg.perm' print(x,...) ## S3 method for class 'cpg.perm' sort(x,decreasing,...)
x 
Output from 
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 
popup.pdf 

main.title 
Main title to be put on the graph. If 
eps.size 
Vector indicating the size of .eps file (if creating one). Correponds to the options horizontal and height in the

tplot 
Logical. If 
perm.ci 
Logical. If 
classic 
Logical. If 
gc.p.val 
Logical. If true, plot will use the genomic control adjusted pvalues. 
gcdisplay 
Logical.If true, plot will display the genomic control value in the legend. 
object 
Output of class 
decreasing 
logical. Should the sort be increasing or decreasing? Not available for partial sorting. 
... 
Arguments to be passed to methods, such as graphical parameters. 
Empirical confidence intervals will be computed only if there are a hundred or more permutations. Otherwise the theoretical confidence intervals will be plotted.
Barfield, R.; Kilaru,V.; Conneely, K.
Maintainer: R. Barfield: <rbarfield01@fas.harvard.edu>
cpg.perm
plot.cpg
scatterplot
manhattan
cpg.assoc
data(samplecpg,samplepheno,package="CpGassoc") ##We will do the analysis on a subset to save time ###NOTE: If you are dealing with large data, do not specify large.data=FALSE. ###The default option is true. ##This will involve partitioning up the data and performing more gc() to clear up space #The qq plot: Testperm<cpg.perm(samplecpg[1:300,],samplepheno$weight,seed=2314,nperm=10,large.data=FALSE) plot(Testperm) #The tstatistic plot from cpg.perm has confidence intervals since we were allowed #to perform permutations on the Tvalues. plot(Testperm,tplot=TRUE) #If there was 100 or more permutations, there would be emperical confidence intervals. #Getting an example of the non classic QQ plot plot(Testperm,classic=FALSE) ###Now for Sort head(sort(Testperm)$results) head(Testperm$results)