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dhsrmethtools

R package with utility functions for converting methylation data to bsseq objects, performing differential methylation analysis, and filtering DMRs.

Installation

devtools::install_github("dhslab/dhsrmethtools")

Usage

library(dhsrmethtools)

Custom functions

  • bed2bsseq()
    Converts simplified bed files with methylation data to bsseq objects.

  • modkit2bsseq()
    Converts ONT bedmethyl files to bsseq objects.

  • pbcpg2bsseq()
    Converts pb-CpG tools bedmethyl files to bsseq objects.

  • hapBSseq()
    Creates bsseq objects from haplotype-specific and combined bedmethyl files based on platform type.

  • callHapDmrs()
    Performs differential methylation analysis between two haplotypes within the same sample.

  • callDmrs()
    Conducts differential methylation analysis between a sample and a normal reference, identifying DMRs.

  • filterHapDmrs()
    Filters haplotype-specific DMRs based on various criteria, optionally comparing against a normal sample.

  • filterDmrs()
    Filters DMRs based on coverage, methylation differences, and other criteria.

  • inferGRanges()
    Infers GRanges objects from files or data frames, supporting various input formats.

To-Do List

  • Update callHapDmrs function to include cpg and length parameters
  • Update filterHapDmrs function
  • Update documentation