testfunc {IMA}R Documentation

Differential methylation testing function

Description

Choose the testing function for differential methylation inference

Usage

testfunc(eset, concov = c("ON", "OFF"), testmethod = c("wilcox","limma", "pooled",
"satterthwaite", "paired"), Padj = c("holm", "hochberg", "hommel","bonferroni", 
"BH", "BY","fdr", "none"), groupinfo, gcase = "g1", gcontrol = "g2", paired = FALSE)

Arguments

eset

a beta value matrix

concov

if "ON", covariates is continuous variable, and "grouplev" should be the continuous values.

testmethod

Wilcoxon rank-sum test (default), Student's t-test ("pooled" or "satterthwaite"), or empirical Bayes statistics.

Padj

The methods available for multiple testing correction. Users could choose any method provided in the p.adjust function of R stat package.

groupinfo

phenotype information for each sample

gcase

the string names of case group/groups in the sample.txt file

gcontrol

the string names of control group/groups in the sample.txt file

paired

if TRUE, the test method would change to the corresponding paired-test method

Value

return a matrix with "P-Value", "Adjust Pval","beta-Difference" in separate columns for each site or annotated region

Author(s)

Dan Wang, Li Yan, Qiang Hu, Dominic J Smiraglia, Song Liu

Maintainer: Dan Wang <wangdan412@gmail.com>

See Also

IMA.methy450R,regionswrapper,IMA.methy450PP,sitetest,indexregionfunc

Examples

# > beta = dataf@bmatrix;##dataf returned by IMA.methy450PP()
# > betar= indexregionfunc(indexlist=dataf@TSS1500Ind,beta=beta,indexmethod="mean")
# > TSS1500testALL = testfunc(eset =betar,testmethod="limma",Padj="BH",concov="OFF",
# + groupinfo = dataf2@groupinfo,gcase ="g1",gcontrol="g2",paired = TRUE)


[Package IMA version 3.1.2 Index]