DMRIntTk: Integrating different DMR sets based on density peak clustering.

ABSTRACT:

Background

Identifying differentially methylated regions (DMRs) is a basic task in DNA methylation analysis. However, due to the different strategies adopted, different DMR sets will be predicted on the same dataset, which poses a challenge in selecting a reliable and comprehensive DMR set for downstream analysis.

Results

Here, we develop DMRIntTk, a toolkit for integrating DMR sets predicted by different methods on a same dataset. In DMRIntTk, the genome is segmented into bins, and the reliability of each DMR set at different methylation thresholds is evaluated. Then, the bins are weighted based on the covered DMR sets and integrated into final DMRs using a density peak clustering algorithm. To demonstrate the practicality of DMRIntTk, it was applied to different scenarios,

SUBMITTER: Zhang W 

PROVIDER: S-EPMC11666043 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature