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https://github.com/dhslab/dhsrmethtools

R functions for methylation analysis

https://github.com/dhslab/dhsrmethtools

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Repository

R functions for methylation analysis

Basic Info
  • Host: GitHub
  • Owner: dhslab
  • License: other
  • Language: R
  • Default Branch: main
  • Size: 355 KB
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  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

dhsrmethtools

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

Installation

R 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

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

Owner

  • Name: Code and Software from David Spencer's lab
  • Login: dhslab
  • Kind: organization
  • Email: dspencerlab@gmail.com
  • Location: United States of America

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Dependencies

DESCRIPTION cran
  • GenomicRanges * imports
  • HDF5Array * imports
  • IRanges * imports
  • bsseq * imports
  • data.table * imports