Python package for DMseg: detecting differential methylation regions in DNA methylome data
Project description
### 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:
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.
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.
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
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