regionswrapper {IMA}R Documentation

Differential methylation testing on all 11 categories of annotated region

Description

This function will output all the differential methylation testing results for the 11 categories of annotated regions, and store the results in the separated sheets of an excel file.

Usage

regionswrapper(dataf, indexmethod = c("mean", "median", "tbrm"), gcase = "g2", 
gcontrol = "g1", testmethod = c("wilcox", "limma", "pooled", "satterthwaite"), 
Padj = "BH", concov = c("OFF", "ON"), paired = FALSE, list11excel, list11Rdata, 
rawpcut = NULL, adjustpcut = NULL, betadiffcut = NULL)

Arguments

dataf

a methy450batch class returned by the IMA.methy450PP function

indexmethod

the methods available to derive an index of overall methylation level for each region

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

testmethod

the available methods include 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.

concov

if "ON", covariates is continuous variable, and the linear model would be used for testing the association between methylation level and continuous phenotype (e.g., age).

paired

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

list11excel

the name of output excel file containing the differential testing results for each annotated region

list11Rdata

the name of output Rdata containing the differential testing result for each annotated region

rawpcut

either null or the output cut-off for the raw p-value

adjustpcut

either null or the output cut-off for the adjusted p-value

betadiffcut

either null or the output cut-off for the beta value difference between two groups

Value

Return an excel file containing the differential testing result for each annotated region as well as an Rdata file containing the differential testing result for each annotated region

Author(s)

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

Maintainer: Dan Wang <wangdan412@gmail.com>

See Also

IMA.methy450PP,IMA.methy450R,testfunc,sitetest,indexregionfunc,annotfunc

Examples

setwd(system.file("extdata", package="IMA"))
MethyFileName = "SampleMethFinalReport.txt"
PhenoFileName = "SamplePhenotype.txt"
data = IMA.methy450R(fileName = MethyFileName,columnGrepPattern=list(beta=".AVG_Beta",detectp=".Detection.Pval"),groupfile = PhenoFileName);
dataf = IMA.methy450PP(data,na.omit = TRUE,normalization=FALSE,transfm = FALSE,samplefilterdetectP = 1e-5,samplefilterperc = 0.75,sitefilterdetectP = 0.05,sitefilterperc=0.75,locidiff = FALSE, XYchrom = FALSE,snpfilter=FALSE ) 
regionswrapper(dataf,indexmethod="mean",gcase="g2",gcontrol="g1",testmethod="limma",Padj="BH",concov="OFF",paired=FALSE,list11excel="./test1.xls",list11Rdata="./test.Rdata",rawpcut = NULL,adjustpcut =NULL,betadiffcut = NULL)

[Package IMA version 3.1.2 Index]