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Epigenome-Wide Association study Software EWAS

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Identifies the disease-related methylecomtypes. EWAS is based on the framework of haplotype-based association study in Haploview extended to DNA methylation data. The tool can (1) calculate the DNA methylation disequilibrium (MD) coefficient between two CpG loci; (2) identify the MD blocks across the whole genome; (3) carry out case-control association study of methylecomtypes and identify the disease-related methylecomtypes.

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1 user review

Yongshuai Jiang's avatar image

Yongshuai Jiang

I/O command
-input(inFile) The input file name
-output(outFile) The output file name
-sort Sort the DNA methylation loci
-unsort Start analysis without sorting the DNA methylation loci
EWAS for single DNA methylation loci
phenotypes vs. beta-value [note: input beta-value]
-t.test Case-control association t-test(case/control or binomial phenotype)
-linear Carry out linear regression analysis (continuous phenotype)
-cor Calculate the Pearson's correlation coefficients (continuous phenotype)
-logistic Carry out logistic regression analysis(case/control or binomial phenotype)
phenotypes vs. SMP (MM MU UU) [note: input beta-value or SMP meplotypes: MM/MU/UU)]
-SMP.convert Convert DNA methlytion beta-value to SMP menoypte (MM MU or UU)
-SMP.allele_chisq Chisq-square test for SMP meplotypes 2 (phenotype)*2 ( M vs. U) table
-SMP.aa Identify the type of SMP allele association for each DNA methylation loci
-SMP.HW Calculate the MAF and Hady-Weinberg pvalue for each DNA methylation loci
-SMP.summary Give a summary statistic for each DNA methylation loci
EWAS for methylocomtype
-methylocomtype Calculate the frequency of methylecomtypes in MD block rigion
-gblock Identify the MD blocks and calculate the frequency of methylecomtype
-gMD Sort the DNA methylation loci
EWAS Meta-analysis
1.4.1 -meta Carry out epigenome wide meta-analysis
Other option list
-gMDFormat('list' or 'matrix') Calculate the frequency of methylecomtypes in MD block rigion(default:'matrix')
-WindowSize(windowSize) The sliding window's size(default:20)
-threshold(a number) Specify a threshold to change the beta-values into two level(H and L)
-unsort Do not sort the DNA methylation loci

EWAS forum

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EWAS versioning

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EWAS classification

EWAS specifications

Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Input format:
CSV
Programming languages:
Java
Version:
1.0
Requirements:
JRE
Source code URL:
http://www.bioapp.org/ewas/file/ewas_complete.tar.gz

EWAS support

Maintainers

Credits

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Publications

Institution(s)

College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China; Training Center for Students Innovation and Entrepreneurship Education of Harbin Medical University, Harbin, China; Department of Ophthalmology, the Second Affiliated Hospital, Harbin Medical University, Harbin, China; Department of Nephrology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China

Funding source(s)

Supported in part by the National Natural Science Foundation of China (Grant No. 31200934) and the Natural Science Foundation of Heilongjiang Province, China (Grant No. C2016036).

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