cpg.combine: Combine various objects of class '"cpg"'

In CpGassoc: Association Between Methylation and a Phenotype of Interest

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 between the various objects (i.e. analysis wasn't performed on the same sites twice).

Usage

cpg.combine(allvalues, fdr.method="BH",fdr.cutoff=.05,return.data=FALSE)

Arguments

allvalues	A list containing the "cpg" objects that are desired to be consolidated.
fdr.method	FDR method that user wants to use. For options see the cpg.assoc help page.
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.
return.data	Logical. cpg.assoc can return dataframes containing the the variable of interest, covariates, and the chip id (if present). Defaults to FALSE. Set to TRUE if plan on using the downstream scaterrplot functions).

Value

info.data

An object of class "cpg" that is the consolidated version of the objects of class cpg that were passed in.

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: <[e-mail]>

See Also

cpg.assoc cpg.perm cpg.work plot.cpg scatterplot manhattan plot.cpg.perm

Examples

data(samplecpg,samplepheno,package="CpGassoc")
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
      

CpGassoc documentation built on Sept. 11, 2024, 5:17 p.m.