sitetest {IMA}R Documentation

Site-level Differential Methylation Analysis

Description

For each specific site, Wilcoxon rank-sum test (default), Student's t-test ("pooled" or "satterthwaite") and empirical Bayes statistics are available for inference in differential testing. Robust linear regression is available as an option to infer methylation change associated with continuous variable (e.g., age). A variety of multiple testing correction algorithms is available, including conservative Bonferroni correction and more liberal false discovery rate control. Users can specify the significance criteria in the parameter file.

Usage

sitetest(dataf, gcase = "g2", gcontrol = "g1", testmethod = c("wilcox", "limma", 
"pooled", "satterthwaite"), Padj = "BH", concov = "OFF", rawpcut = NULL, 
adjustpcut = NULL, betadiffcut = NULL, paired = FALSE)

Arguments

dataf

a methy450batch class returned by the IMA.methy450PP function

gcase

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

gcontrol

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

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.

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).

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

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

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,testfunc,indexregionfunc

Examples

# >sitetest = sitetest(dataf,gcase="g2",gcontrol="g1",testmethod = "mean",
# +Padj="BH",rawpcut = NULL,adjustpcut =NULL,betadiffcut = NULL,paired=FALSE)

[Package IMA version 3.1.2 Index]