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