cpg.combine {CpGassoc} | R Documentation |
Combine various objects of class "cpg"
Description
Takes a list containing objects of class "cpg"
and combines them into one cpg item. Assumes that there are no repeated CpG sites bewtween the various objects (i.e. analysis wasn't performed on the same sites twice).
Usage
cpg.combine(allvalues, fdr.method="BH",fdr.cutoff=.05)
Arguments
allvalues |
A list containing the |
fdr.method |
FDR method that user wants to use. For options see the |
fdr.cutoff |
The desired FDR threshold. The default setting is .05. The set of CpG sites with FDR < fdr.cutoff will be labeled as significant. |
Value
info.data |
An object of class |
Note
This is designed to be used by cpg.assoc
when it does analysis on large data sets or by the user if they split up the analysis by chromosome or some other such partition.
Author(s)
Barfield, R.; Kilaru,V.; Conneely, K.
Maintainer: R. Barfield: <rbarfield01@fas.harvard.edu>
See Also
cpg.assoc
cpg.perm
cpg.work
plot.cpg
scatterplot
manhattan
plot.cpg.perm
Examples
data(samplecpg,samplepheno,package="CpGassoc")
###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
test1<-cpg.assoc(samplecpg[1:100,],samplepheno$weight,large.data=FALSE)
test2<-cpg.assoc(samplecpg[101:200,],samplepheno$weight,large.data=FALSE)
bigtest<-list(test1,test2)
overall<-cpg.combine(bigtest)
overall