Skip to main content

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:

  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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

DMseg-1.0.2.tar.gz (7.6 kB view details)

Uploaded Source

Built Distribution

DMseg-1.0.2-py3-none-any.whl (7.7 kB view details)

Uploaded Python 3

File details

Details for the file DMseg-1.0.2.tar.gz.

File metadata

  • Download URL: DMseg-1.0.2.tar.gz
  • Upload date:
  • Size: 7.6 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.8.0 pkginfo/1.8.2 readme-renderer/32.0 requests/2.25.1 requests-toolbelt/0.9.1 urllib3/1.26.4 tqdm/4.59.0 importlib-metadata/3.10.0 keyring/22.3.0 rfc3986/2.0.0 colorama/0.4.4 CPython/3.8.8

File hashes

Hashes for DMseg-1.0.2.tar.gz
Algorithm Hash digest
SHA256 55faff8542d9f445ec8281561ecd2057545f107bffe83a90866e1f6d5bd9b35d
MD5 f2ea97f381634ad3fea77b37aa5d86e0
BLAKE2b-256 132f63850650b05873322f04450a36a50283b48e223d651cec37a618a7effaf1

See more details on using hashes here.

Provenance

File details

Details for the file DMseg-1.0.2-py3-none-any.whl.

File metadata

  • Download URL: DMseg-1.0.2-py3-none-any.whl
  • Upload date:
  • Size: 7.7 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.8.0 pkginfo/1.8.2 readme-renderer/32.0 requests/2.25.1 requests-toolbelt/0.9.1 urllib3/1.26.4 tqdm/4.59.0 importlib-metadata/3.10.0 keyring/22.3.0 rfc3986/2.0.0 colorama/0.4.4 CPython/3.8.8

File hashes

Hashes for DMseg-1.0.2-py3-none-any.whl
Algorithm Hash digest
SHA256 17b09d1091d2968d3d6587d37a3003e74c7612b5d2ab3a53932b87f025e13b45
MD5 ef280ecf6c2c403ac270304207757262
BLAKE2b-256 7fdbd31c7e4e476bcbb1ba63ee17b91b14cbeb8f542bb0e1db43dd47008d8b7e

See more details on using hashes here.

Provenance

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page