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RefFreeEWAS specifications

Information


Unique identifier OMICS_13675
Name RefFreeEWAS
Alternative names RefFree Epigenome-Wide Association Studies, RefFreeCellMix
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 2.1
Stability Stable
Requirements
quadprog, R(≥3.2.2), isva
Maintained Yes

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Documentation


Maintainers


  • person_outline Andres Houseman
  • person_outline Andres Houseman

Publications for RefFree Epigenome-Wide Association Studies

RefFreeEWAS citations

 (13)
library_books

DNA Methylation and Body Composition in Preschool Children: Epigenome Wide Analysis in the European Childhood Obesity Project (CHOP) Study

2017
Sci Rep
PMCID: 5662763
PMID: 29084944
DOI: 10.1038/s41598-017-13099-4

[…] n in any case, as references derived from blood may not reflect the tissue-specificity of methylation of adipose tissue as discussed already above. However, using Houseman’s new reference free model “RefFreeEWAS”, with K = 9 latent dimensions to account for potential collinearity of the phenotype and or covariates within the methylation value matrix, resulted in our study in an over-adjustment ind […]

library_books

Deconvolution of DNA methylation identifies differentially methylated gene regions on 1p36 across breast cancer subtypes

2017
Sci Rep
PMCID: 5599639
PMID: 28912426
DOI: 10.1038/s41598-017-10199-z

[…] models. To analyze DNAm differences between tumor and normal tissue and to adjust for effects of cellular heterogeneity across samples, we applied the reference-free deconvolution algorithm from the RefFreeEWAS R package to each model adjusting for age. The method estimates the number of underlying tissue-specific cell methylation states contributing to methylation heterogeneity through a constra […]

library_books

Normal breast tissue DNA methylation differences at regulatory elements are associated with the cancer risk factor age

2017
PMCID: 5504720
PMID: 28693600
DOI: 10.1186/s13058-017-0873-y

[…] stical methods that account for cell proportion variability across tissue samples without a reference DNA methylome have been widely used [, –]. To perform a reference-free EWAS we used the R package RefFreeEWAS to deconvolute the cellular populations present in the tissue biopsy samples using DNA methylation data as detailed previously in Houseman et al. []. Briefly, this method seeks to represen […]

library_books

Comparison of different cell type correction methods for genome scale epigenetics studies

2017
BMC Bioinformatics
PMCID: 5391562
PMID: 28410574
DOI: 10.1186/s12859-017-1611-2

[…] in Fig. . Further comparisons indicated that CpG site cg10662395 was also identified by RefFreeCellMix and RUV, and was the only CpG site to overlap among all seven analyses (Houseman et al., minfi, RefFreeEWAS, SVA, RefFreeCellMix and RUV, as well as the analyses without adjusting for cell types). Although ReFACTor identified the largest number of CpGs, they did not overlap with the joint findin […]

library_books

Genome Wide Methylation Analysis Identifies Specific Epigenetic Marks In Severely Obese Children

2017
Sci Rep
PMCID: 5384222
PMID: 28387357
DOI: 10.1038/srep46311

[…] To correct our methylation data analysis for cell heterogeneity between samples, we used R package RefFreeEwas. This package allows for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types. This method is similar to surrogate variable analysis, except that it makes […]

call_split

Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies

2017
Genome Biol
PMCID: 5267453
PMID: 28122605
DOI: 10.1186/s13059-016-1143-5
call_split See protocol

[…] oposed DM calling method to all TCGA data whenever the 450 k data were available. We compared the DMC calling results with minfi [], arguably the most widely used package for 450 k data analysis, and RefFreeEWAS, which considers cell composition in DM calling. We ran minfi using default parameters and specified K = 2 in RefFreeEWAS, corresponding to two components (cancer and normal) in the cell m […]

Citations

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RefFreeEWAS institution(s)
School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA; Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Department of Pathology, University of Miami, Miller School of Medicine, Miami, FL, USA; Department of Epidemiology, Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA; Department of Community and Family Medicine, Dartmouth Medical School, Hanover, NH, USA
RefFreeEWAS funding source(s)
This work was supported by the National Institutes for Health (grants n°NIMH R01-MH094609, NIEHS P01-ES022832, K01-ES017800, R01-ES024991 and R01-ES015533); the Environmental Protection Agency (grant n°RD83544201).

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