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

Dan Wang; Li Yan; Qiang Hu; Lara E. Sucheston; Michael J. Higgins; Christine B. Ambrosone; Candace S. Johnson; Dominic J. Smiraglia; Song Liu

doi:10.1093/bioinformatics/bts013

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

Dan Wang
, Li Yan
, Qiang Hu
, Lara E. Sucheston
, Michael J. Higgins
, Christine B. Ambrosone
, Candace S. Johnson
, Dominic J. Smiraglia
, Song Liu

Department of Biostatistics

Roswell Park Cancer Institute

Research output: Contribution to journal › Article › peer-review

259 Scopus citations

Abstract

Summary: 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 usercustomized functions commonly required to perform exploratory methylation analysis for individual sites as well as annotated regions.

Original language	English
Article number	bts013
Pages (from-to)	729-730
Number of pages	2
Journal	Bioinformatics
Volume	28
Issue number	5
DOIs	https://doi.org/10.1093/bioinformatics/bts013
State	Published - Mar 2012

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10.1093/bioinformatics/bts013

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title = "IMA: An R package for high-throughput analysis of Illumina's 450K Infinium methylation data",

abstract = "Summary: 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 usercustomized functions commonly required to perform exploratory methylation analysis for individual sites as well as annotated regions.",

author = "Dan Wang and Li Yan and Qiang Hu and Sucheston, \{Lara E.\} and Higgins, \{Michael J.\} and Ambrosone, \{Christine B.\} and Johnson, \{Candace S.\} and Smiraglia, \{Dominic J.\} and Song Liu",

year = "2012",

month = mar,

doi = "10.1093/bioinformatics/bts013",

language = "English",

volume = "28",

pages = "729--730",

journal = "Bioinformatics",

issn = "1367-4803",

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T2 - An R package for high-throughput analysis of Illumina's 450K Infinium methylation data

AU - Wang, Dan

AU - Yan, Li

AU - Hu, Qiang

AU - Sucheston, Lara E.

AU - Higgins, Michael J.

AU - Ambrosone, Christine B.

AU - Johnson, Candace S.

AU - Smiraglia, Dominic J.

AU - Liu, Song

PY - 2012/3

Y1 - 2012/3

N2 - Summary: 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 usercustomized functions commonly required to perform exploratory methylation analysis for individual sites as well as annotated regions.

AB - Summary: 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 usercustomized functions commonly required to perform exploratory methylation analysis for individual sites as well as annotated regions.

UR - https://www.scopus.com/pages/publications/84863230488

U2 - 10.1093/bioinformatics/bts013

DO - 10.1093/bioinformatics/bts013

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EP - 730

JO - Bioinformatics

JF - Bioinformatics

IS - 5

M1 - bts013

ER -

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

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