EWAS specifications

Information


Unique identifier OMICS_18612
Name EWAS
Alternative name Epigenome-Wide Association study Software
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format CSV
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 2.0
Stability Stable
Requirements JRE
Maintained Yes

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Maintainers


  • person_outline Yongshuai Jiang <>
  • person_outline Lijun Yuan <>
  • person_outline Fanwu Kong <>
  • person_outline Liangde Xu <>

EWAS articles

EWAS institution(s)
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China; Training Center for Students Innovation and Entrepreneurship Education, Harbin Medical University, Harbin, China; Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China; Department of Mathematics, Harbin Institute of Technology, Harbin, China; College of Life Science, Northwest A&F University, Yangling, China; Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, Harbin, China; Department of Nephrology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
EWAS funding source(s)
Supported in part by the National Natural Science Foundation of China (Grant Nos. 91746113, 81601422, 81600403, 81701350, 31501062) and the Basic Research Program of Shenzhen (JCYJ20160229203627477).

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Desktop
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