IMA.methy450R {IMA}R Documentation

Load methylation 450k data

Description

This function will load the methylation 450k data. The input information for the package consists basically of two files containing beta-value methylation data (including annotation) produced by BeadStudio or GenomeStudio, and sample phenotype data prepared by the user. IMA.methy450R function loads the input files with a single command described below and an exprmethy450 object will be created, which includes the following features: beta value matrix, locus annotation, detection P-value and sample phenotype information. Besides, basic quality control information will be outputted in the QC.pdf, which include unsupervised sample clustering using all loci, boxplot for beta value of each sample, and barplot showing the percent of loci with detection P-value smaller than 1e-5 in each sample.

Usage

IMA.methy450R(fileName, columnGrepPattern = list(beta = ".AVG_Beta",
 detectp = ".Detection.Pval"), groupfile,...)

Arguments

fileName

This is the input file containing the 450k methylation data including β value, detection p-value and loci annotation information. This file can be be produced from the illumina BeadStudio or GenomeStudio software.

columnGrepPattern

Specify the columns with corresponding characters within the 450k methylation data file produced by illumina BeadStudio or GenomeStudio software. These columns will be loaded into the function.

groupfile

This is the input file containing the phenotype data prepared by the users.

...

Arguments in read.delim(), such as parameter "sep" could be set to sep="," if the GenoneStudio file is separated by comma instead of tab.

Value

This function will return an exprmethy450 class including these features: a β value matrix, an annotation matrix, a detection p-value matrix and a list of sample phenotype information. A QC.pdf file including the basic quality control information will be generated.

bmatrix

the β value matrix for each site in each sample

detectP

a matrix of detection p-value for each site in each sample

annot

a matrix of annotation information for each targeted site

groupinfo

a matrix of sample ID and phenotype information for each sample

Author(s)

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

Maintainer: Dan Wang <wangdan412@gmail.com>

See Also

IMA.methy450PP,regionswrapper,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);

[Package IMA version 3.1.2 Index]