EWAS   2.0

EWAS for single DNA methylation loci

Phenotypes vs. Beta-value

T test

EWAS can carry out T test for single DNA methylation locus and calculate the Tp values

 

input file ：

please see example_ewas.txt or download example_ewas.zip for more information.

 

• The first row in EWAS input data file is the header line. From the fourth to the last is the status of sample.

From the fourth to the last:
        0: unknown/miss
        1: unaffected/normal/control group
        2: affected/disease/case group

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 3: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 4 to end: (e.g. 0.492 0.708 0.483 etc.) represents the beta-value of samples in the DNA methylation locus.

 

OutFile ：

 

• Column information:
        

column 1: the ID of the DNA methylation locus.
column 2: chromosome number.
column 3: physical position of the DNA methylation locus.
column 4: the number of valid case samples.
column 5: the number of valid control samples.
column 6: the average of DNA methylation level in case samples.
column 4: the average of DNA methylation level in control samples.
column 5: Fold change.
column 6: T statistic.
column 7: p value.

Simple linear regression

EWAS can Carry out simple linear regression analysis for each methylation loci with continuous phenotypes.

 

 

input file ：

please see example_linear.txt or download example_linear.zip for more information.

 

• The first row in EWAS input data file is the header line. From the fourth to the last is the continuous phenotype of sample, such as : age

 

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 3: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 4 to end: (e.g. 0.492 0.708 0.483 etc.) represents the beta-value of samples in the DNA methylation locus.

 

OutFile ：

 

• Column information:
        

column 1: the ID of the DNA methylation locus.
column 2: chromosome number.
column 3: physical position of the DNA methylation locus.
column 4: total sample number.
column 5: valid sample number.
column 6: missing rate.

column 7: linear regression coefficient.

column 8: standard error.
column 9: p value.

logistic regression

EWAS can Carry out logistic regression analysis for each methylation loci with binomial phenotype.

 

 

input file ：

please see example_logistic.txt or download example_logistic.zip for more information.

 

• The first row in EWAS input data file, with a phenotype name starting with "#",is the header line. From the fourth to the last is the phenotype of sample, such as disease state.
  1: case
  0: control

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.
form column 2 to end: (e.g. 0.492 0.708 0.483 etc.) represents the beta-value of samples in the DNA methylation locus.

OutFile ：

 

• Column information:
        

column 1: the ID of the DNA methylation locus.
column 2: total sample number.
column 3: valid sample number.
column 4: intercept.
column 5: standard error of intercept.
column 6: Zvalue of intercept.
column 7: Pvalue of intercept.
column 8: marker's logistic regression coefficient.
column 9: standard error of marker's logistic regression coefficient.
column 10: Zvalue of logistic marker's regression coefficient.
column 11: p value of logistic marker's regression coefficient.


 

Calculate the Pearson's correlation coefficients

EWAS can Calculate the Pearson's correlation coefficients for each methylation loci with continuous phenotype.

 

 

input file ：

please see example_cor.txt or download example_cor.zip for more information.

 

• The first row in EWAS input data file is the header line. From the fourth to the last is the continuous phenotype of sample, such as : age

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 3: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 4 to end: (e.g. 0.492 0.708 0.483 etc.) represents the beta-value of samples in the DNA methylation locus.

OutFile ：

 

• Column information:
        

column 1: the ID of the DNA methylation locus.
column 2: chromosome number.
column 3: physical position of the DNA methylation locus.
column 4: total sample number.
column 5: valid sample number.
column 6: missing rate.

column 7: Pearson's correlation coefficient.

column 8: 95% CI of Pearson's correlation coefficient.

column 9: z value.

column 10: 95% CI of z value.

column 11: standard error of z value.
column 12: p value of z value.

 

Phenotypes vs. SMP(MM MU UU)

Convert DNA methlytion beta-value to SMP menoypte

EWAS can Convert DNA methlytion beta-value to SMP menoypte use two threshold.

 

 

input file ：

please see example_ewas.txt or download example_ewas.zip for more information.

 

• The first row in EWAS input data file is the header line. From the fourth to the last is the status of sample.

          0: unknown/miss
          1: unaffected/normal/control group
          2: affected/disease/case group

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 3: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 4 to end: (e.g. 0.492 0.708 0.483 etc.) represents the beta-value of samples in the DNA methylation locus.

OutFile ：

 

 

• The first row in EWAS input data file is the header line. From the fourth to the last is the status of sample.
          0: unknown/miss
          1: unaffected/normal/control group
          2: affected/disease/case group

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information. For more example data, see: out_smp.txt.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 3: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 4 to end: (e.g. MU etc.) represents the mplotype of samples in the DNA methylation locus.

 

Chisq-square test for SMP methylation alleles

EWAS can Carry out Chisq-square test for SMP meplotypes , 2 (phenotype)*2 ( M vs. U) table.

 

 

input file ：

please see out_smp.txt or download out_smp.zip for more information.

 

 

• The first row in EWAS input data file is the header line. From the fourth to the last is the status of sample.
          0: unknown/miss
          1: unaffected/normal/control group
          2: affected/disease/case group

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information. For more example data, see: out_smp.txt.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 3: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 4 to end: (e.g. MU etc.) represents the methylation genotype of samples in the DNA methylation locus.

 

OutFile ：

 

• Column information:
        

column 1: the ID of the DNA methylation locus.
column 2: chromosome number.
column 3: physical position of the DNA methylation locus.
column 4: total sample number.
column 5: case sample number.

column 6: control sample number.

column 7: missing sample number.

column 8: case M number.

column 9: control M number.

column 10: case U number.

column 11: control U number.

column 12:chisqure statistic.
column 13:chisqure p value.

column 14: OR.

column 15: 95% CI.

Attention:	for one SMP , if		case	control
		M	a	b
		U	c	d

 

	then,    OR=(a/c)/(b/d)=ad/bc
		OR>1,   risk factor
		OR=1,   has no effect
		OR<1,   protective factor

 

 

SMP allele association

EWAS can Identify the type of SMP allele association for each DNA methylation loci.

 

 

input file ：

please see out_smp.txt or download out_smp.zip for more information.

 

 

• The first row in EWAS input data file is the header line. From the fourth to the last is the status of sample.
          0: unknown/miss
          1: unaffected/normal/control group
          2: affected/disease/case group

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information. For more example data, see: out_smp.txt.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 3: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 4 to end: (e.g. MU etc.) represents the mplotype of samples in the DNA methylation locus.

 

OutFile ：

 

• Column information:
        

column 1: the ID of the DNA methylation locus.
column 2: chromosome number.
column 3: physical position of the DNA methylation locus.
column 4: total sample number.
column 5: total sample number with unkown information.

column 6: case sample number with unkown information.

column 7: control sample number with unkown information.

column 8: total number ratio with MM meplotype.

column 9: case number ratio with MM meplotype.

column 10: control number ratio with MM meplotype.

column 11: total number ratio of M.

column 12: case number ratio of M.

column 13: control number ratio of M.

column 14: SMP association type.

column 15: case SMP association type.

column 16: control SMP association type.

MAF and Hardy-Weinberg

EWAS can Calculate the MAF and Hady-Weinberg pvalue for each DNA methylation loci.

 

 

input file ：

please see out_smp.txt or download out_smp.zip for more information.

 

 

• The first row in EWAS input data file is the header line. From the fourth to the last is the status of sample.
          0: unknown/miss
          1: unaffected/normal/control group
          2: affected/disease/case group

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information. For more example data, see: out_smp.txt.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 3: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 4 to end: (e.g. MU etc.) represents the mplotype of samples in the DNA methylation locus.

 

OutFile ：

 

                column 1-11:

 

                column 12-22:

• Column information:
        

column 1: the ID of the DNA methylation locus.
column 2: chromosome number.
column 3: physical position of the DNA methylation locus.
column 4: total sample number.
column 5: all sample number with unkown meplotype.
column 6: case sample number with unkown meplotype.

column 7: control sample number with unkown meplotype.

column 8: all sample number with MM meplotype.
column 9: case sample number with MM meplotype.

column 10: control sample number with MM meplotype.

column 11: all sample number with MU meplotype.
column 12: case sample number with MU meplotype.

column 13: control sample number with MU meplotype.

column 14: all sample number with UU meplotype.
column 15: case sample number with UU meplotype.

column 16: control sample number with UU meplotype.

column 17: MAF.
column 18: case MAF.

column 19: control MAF.

column 20: Hady-Weinberg p value.
column 21: case Hady-Weinberg p value.

column 22: control Hady-Weinberg p value.

Summary statistic

EWAS can Give a summary statistic for each DNA methylation loci.

 

 

input file ：

please see out_smp.txt or download out_smp.zip for more information.

 

 

• The first row in EWAS input data file is the header line. From the fourth to the last is the status of sample.
          0: unknown/miss
          1: unaffected/normal/control group
          2: affected/disease/case group

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information. For more example data, see: out_smp.txt.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 3: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 4 to end: (e.g. MU etc.) represents the mplotype of samples in the DNA methylation locus.

 

OutFile ：

 

                column 1-16:

 

                column 17-31:

• Column information:
        

column 1: the ID of the DNA methylation locus.
column 2: chromosome number.
column 3: physical position of the DNA methylation locus.
column 4: total sample number.

column 5: all sample number with unkown meplotype.
column 6: case sample number with unkown meplotype.

column 7: control sample number with unkown meplotype.

column 8: all sample number with MM meplotype.
column 9: case sample number with MM meplotype.

column 10: control sample number with MM meplotype.

column 11: all sample number with MU meplotype.
column 12: case sample number with MU meplotype.

column 13: control sample number with MU meplotype.

column 14: all sample number with UU meplotype.
column 15: case sample number with UU meplotype.

column 16: control sample number with UU meplotype.

column 17: MAF.
column 18: case MAF.

column 19: control MAF.

column 20: Hady-Weinberg p value.
column 21: case Hady-Weinberg p value.

column 22: control Hady-Weinberg p value.

column 23: total number ratio with MM meplotype.

column 24: case number ratio with MM meplotype.

column 25: control number ratio with MM meplotype.

column 26: total number ratio of M.

column 27: case number ratio of M.

column 28: control number ratio of M.

column 29: SMP association type.

column 30: case SMP association type.

column 31: control SMP association type.

 

 

EWAS for methylation haplotype

Output the results of epigenome-wide meplotype

association study

EWAS can scan the entire genome and identify the association between combinations of methylation levels (meplotype) and diseases.

 

 

input file ：

please see example_meplotype.txt or download example_meplotype.zip for more information.

 

• The first row in EWAS input data file is the header line. From the fourth to the last is the status of sample.

From the fourth to the last:
        0: unknown/miss
        1: unaffected/normal/control group
        2: affected/disease/case group

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. M/U) represents the methylation status of the DNA methylation locus.
column 3: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 4: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 5 to end: (e.g. 0.492 0.708 0.483 etc.) represents the methylation genotype in each sample.

 

OutFile ：

 

column 1-9

 

column 10-15

• Column information:

column 1: block number.

column 2: chromosome number.
column 3: the start position.
column 4: the end position.
column 5: the methylation haplotype.
column 6: the total frequency of the methylation haplotype.
column 7: the frequency of the methylation haplotype in case samples.
column 8: the frequency of the methylation haplotype in control samples.
column 9: the number of this methylation haplotype and others in case samples.
column 10: the number of this methylation haplotype and others in control samples.
column 11: the chi-square statistic.
column 12: the P-value of chi-square test.
column 13: OR.
column 14: 95%CI of OR.
column 15: methylation locis in the blocks.

Attention:	for one meplotype , if		case	control
		this meplotype	a	b
		other meplotype	c	d

 

	then,    OR=(a/c)/(b/d)=ad/bc
		OR>1,   risk factor
		OR=1,   has no effect
		OR<1,   protective factor

 

 

Output the MD coefficient D-prime and r-square

For a list of DNA methylation loci, EWAS can calculate the MD coefficient D-prime and r-square. We provided two types of output formate: matrix and list.

matrix format:

 

input file ：

please see example_md.txt or download example_md.zip for more information.

 

• The first row in EWAS input data file is the header line. From the fifth to the last is the status of sample.

From the fifth to the last:
        0: unknown/miss
        1: unaffected/normal/control group
        2: affected/disease/case group

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. M/U) represents the methylation status of the DNA methylation locus.
column 3: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 4: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 5 to end: (e.g. 0.492 0.708 0.483 etc.) represents the methylation status of samples in the DNA methylation locus.

OutFile ：

 

• The first row and the first colum for each martrix is the DNA methylation loci. The data in the matrix is D-prime or r-square.

list format:

 

OutFile ：

 

• The list format:

column 1: is the ID of the first DNA methylation locus.

column 2: is the ID of the second DNA methylation locus.
column 3: is the MD coefficient D-prime.
column 4: is the MD coefficient and r-square.

Output the MD block

EWAS can identify the MD blocks and calculate the frequency of meplotype in the blocks.

 

 

input file ：

please see example_meplotype.txt or download example_meplotype.zip for more information.

 

• The first row in EWAS input data file is the header line. From the fifth to the last is the status of sample.

From the fifth to the last:
        0: unknown/miss
        1: unaffected/normal/control group
        2: affected/disease/case group

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. M/U) represents the methylation status of the DNA methylation locus.
column 3: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 4: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 5 to end: (e.g. 0.492 0.708 0.483 etc.) represents the methylation status of samples in the DNA methylation locus.

 

OutFile ：

• Column information:
        

column 1: block#.

column 2: chromosome number.
column 3: start position of the block.
column 4: end position of the block.
column 5: the meplotype in blocks.
column 6: frequency of methylecomtype in total sapmles.
column 7: methylation loci in the blocks.

EWAS for methylecomtype

Output the results of epigenome-wide methylecomtype

association study

EWAS can scan the entire genome and identify the association between combinations of methylation levels (methylecomtype) and diseases.

 

 

input file :

please see example_ewas.txt or download example_ewas.zip for more information.

 

• The first row in EWAS input data file is the header line. From the fourth to the last is the status of sample.

From the fourth to the last:
        0: unknown/miss
        1: unaffected/normal/control group
        2: affected/disease/case group

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 3: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 4 to end: (e.g. 0.492 0.708 0.483 etc.) represents the beta-value of samples in the DNA methylation locus.

 

OutFile ：

 

• Column information:

column 1: block#.

column 2: the methylecomtype in blocks.
column 3: chromosome number.
column 4: the start position.
column 5: the end position.
column 6: the total sample number.
column 7: the number of methylecomtype in total sapmles.
column 8: the number of methylecomtype in cases.
column 9: the number of methylecomtype in controls.
column 10: frequency of methylecomtype in total sapmles.
column 11: frequency of methylecomtype in cases.
column 12: frequency of methylecomtype in controls.
column 13: the chi-square statistic.
column 14: the P-value of chi-square test.
column 15: OR.
column 16: 95%CI of OR.
column 17: methylation loci in the blocks.

Attention:	for one meplotype , if		case	control
		this meplotype	a	b
		other meplotype	c	d

 

	then,    OR=(a/c)/(b/d)=ad/bc
		OR>1,   risk factor
		OR=1,   has no effect
		OR<1,   protective factor

 

 

 

Output the general MD coefficient gD-prime

and gr-square

For a list of DNA methylation loci, EWAS can calculate the general MD coefficient gD-prime and gr-square. We provided two types of output formate: matrix and list.

matrix format:

 

input file ：

please see example_gMD.txt or download example_gMD.zip for more information.

 

• The first row in EWAS input data file is the header line. From the fourth to the last is the status of sample.

From the fourth to the last:
        0: unknown/miss
        1: unaffected/normal/control group
        2: affected/disease/case group

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 3: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 4 to end: (e.g. 0.492 0.708 0.483 etc.) represents the beta-value of samples in the DNA methylation locus.

OutFile ：

 

• The first row and the first colum for each martrix is the DNA methylation loci. The data in the matrix is gD-prime or gr-square.

list format:

 

OutFile ：

 

• The list format:

column 1: is the ID of the first DNA methylation locus.

column 2: is the ID of the second DNA methylation locus.
column 3: is the MD coefficient gD-prime.
column 4: is the MD coefficient and gr-square.

Output the general MD block

EWAS can identify the general MD blocks and calculate the frequency of methylecomtype in the blocks.

 

 

input file ：

please see example_gblock.txt or download example_gblock.zip for more information.

 

• The first row in EWAS input data file is the header line. From the fourth to the last is the status of sample.

From the fourth to the last:
        0 unknown/miss
        1: unaffected/normal/control group
        2: affected/disease/case group

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 3: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 4 to end: (e.g. 0.492 0.708 0.483 etc.) represents the beta-value of samples in the DNA methylation locus.

 

OutFile ：

• Column information:
        

column 1: block#.

column 2: the methylecomtype in blocks.
column 3: chromosome number.
column 4: start position of the block.
column 5: end position of the block.
column 6: the total sample number.
column 7: the number of methylecomtype in total sapmles.
column 8: frequency of methylecomtype in total sapmles.
column 9: methylation loci in the blocks.

Output sorted data

We firstly sort the DNA methylation loci based on their physical position. Then change the beta-values into two levels (H: high DNA methylation level and L: low DNA methylation level).

 

 

input file ：

please see example_ewas.txt or download example_ewas.zip for more information.

 

• The first row in EWAS input data file is the header line. From the fourth to the last is the status of sample.
          0: unknown/miss
          1: unaffected/normal/control group
          2: affected/disease/case group

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 3: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 4 to end: (e.g. 0.492 0.708 0.483 etc.) represents the beta-value of samples in the DNA methylation locus.

OutFile ：

 

• The first row in EWAS input data file is the header line. From the fourth to the last is the status of sample.
          0: unknown/miss
          1: unaffected/normal/control group
          2: affected/disease/case group
• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 3: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 4 to end: (e.g. 0.492 0.708 0.483 etc.) represents the beta-value of samples in the DNA methylation locus.

 

meta-analysis

Carry out epigenome wide meta-analysis

EWAS can Give a summary statistic for each DNA methylation loci.

 

 

input file ：

please see example_meta.txt or download example_meta.zip for more information.

 

 

• The first row in EWAS input data file is the header line. From the fourth to the last: every two column represent one study.

• From the second row to the end, One line in EWAS input data file represents a DNA methylation locus information.
        

column 1: (e.g. cg00000165) is the ID or name of a DNA methylation locus.

column 2: (e.g. chr1) represents the chromosome number of the DNA methylation locus.
column 3: (e.g. 91194674) represents physical position of the DNA methylation locus.
form column 4 to end: every two column represent one study, first column is regression coefficients, the next column is its standerd error .

 

OutFile ：

 

• Column information:
        

column   1: the ID of the DNA methylation locus.
column   2: chromosome number.
column   3: physical position of the DNA methylation locus.
column   4: total study number.
column   5: valid study number.
column   6: Q-test statistic.

column   7: Q-test p value.

column   8: I2statistic.
column   9: Pooled effect statistics in fixed model.

column 10: 95% CI of pooled effect statistics in fixed model.

column 11: Standard error of pooled effect statistics in fixed model.

column 12: Z-test statistic of pooled effect statistics in fixed model..

column 13: P value for z-test statistic of pooled effect statistics in fixed model..

column 14: Pooled effect statistics in random model.

column 15: 95% CI of pooled effect statistics in random model.

column 16: Standard error of pooled effect statistics in random model.

column 17: Z-test statistic of pooled effect statistics in random model.

column 18: P value for z-test statistic of pooled effect statistics in random model.

 

Options list

• 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)
    -logistic	Carry out logistic regression analysis(case/control or binomial phenotype)
    -cor	Calculate the Pearson's correlation coefficients (continuous 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 meplotype (methylation haplotype)

  –meplotype	Epigenome-wide meplotype association test
  -MD	Calculated the MD coefficient MD-prime and MD r-square
  -block	Identify the MD blocks and calculate the frequency of meplotype

• EWAS for methylecomtype

  -methylocomtype	Calculate the frequency of methylecomtypes in MD block rigion
  -gMD	calculated the general MD coefficient gD-prime and gr-square
  -gblock	Identify the general MD blocks and calculate the frequency of methylecomtype

• EWAS Meta-analysis

  -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