DMseg 1.0.1

Python package for DMseg: detecting differential methylation regions in DNA methylome data

### DMseg: detecting differential methylation regions (DMRs) in methylome

This is a Python package to search through methylome-side CpGs sites for DMRs between two biological conditions. The algorithm executes the following analysis steps:

1. A linear regression model is fitted to the beta values for each CpG, using the user-input covariates: the first variable is the group label of interest.

2. Nominal p-values from individual CpG associations are used to define the DMR: more than or equal to two consecutive CpGs with p-value <0.05 will be considered as candidate DMR. A likelihood ratio statistic (LRT) is computed for a candidate DMR.

3. Group labels will be permuted for B times, step 1 and 2 are repeated for each permuation dataset. Family-wise error rate is computed using the null distribution of LRT based on permutation.

To install the package:

` python -m pip install DMseg ` To run the python package, one can first port in the package and the core function file DMseg.py, then call the pipeline function DMseg_pipeline

` import DMseg from DMseg import DMseg result = DMseg.DMseg_pipeline(betafile, colDatafile, postionfile, maxgap=500, sd_cutoff=0.025, beta_diff_cutoff=0.05, zscore_cutoff=1.96, B=500, seed=1001) `

The inputs for the function DMseg_pipeline are

• betafile: the file location for the n x p matrix of methylation beta values (n is the number of samples, p is the number of CpG sites)

• colDatafile: the file location for the covariates for regression analysis

• postionfile: the file location for the chromosomal positions of CpGs

• maxgap is the maximal base pairs between two adjacent CpGs that can be considered as within the same DMR

• sd_cutoff is the minimal inter-sample standard deviation for a CpG to be considered for differential methylation

• beta_diff_cutoff is the minimal mean differences between the two comparison groups for a CpG to be considered for differential methylation

• zscore_cutoff is the minimal z-score for a CpG to be considered for differential methylation

• B is the number permutations to compute family-wise error rate

• seed is the seed for the random number generator when permuting the group labels