IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data.

ABSTRACT

UNLABELLED The Illumina Infinium HumanMethylation450 BeadChip is a newly designed high-density microarray for quantifying the methylation level of over 450 000 CpG sites within human genome. Illumina Methylation Analyzer (IMA) is a computational 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. The pipeline loads the data from Illumina platform and provides user-customized functions commonly required to perform exploratory methylation analysis for individual sites as well as annotated regions. AVAILABILITY: IMA is implemented in the R language and is freely available from http//www.rforge.net/IMA.