IMA (Illumina Methylation Analyzer)


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Documentation for package ‘IMA’ version 3.1.2

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IMA-package IMA(Illumina Methylation Analyzer) is a package designed to automate the pipeline for exploratory analysis and summarization of site-level and region-level methylation changes in epigenetic studies utilizing the 450K DNA methylation microarray
annotfunc Annotate siteIDs/regionIDs of interest
exprmethy450 Load methylation 450k data
IMA IMA(Illumina Methylation Analyzer) is a package designed to automate the pipeline for exploratory analysis and summarization of site-level and region-level methylation changes in epigenetic studies utilizing the 450K DNA methylation microarray
IMA.methy450PP Data preprocessing and quality control
IMA.methy450R Load methylation 450k data
indexregionfunc Region-level Methylation Index Calculation
methy450batch Data preprocessing and quality control
outputDMfunc Output the differentially methylated sites/regions
regionswrapper Differential methylation testing on all 11 categories of annotated region
sitetest Site-level Differential Methylation Analysis
testfunc Differential methylation testing function