R package with utility functions for converting methylation data to bsseq
objects, performing differential methylation analysis, and filtering DMRs.
devtools::install_github("dhslab/dhsrmethtools")
library(dhsrmethtools)
-
bed2bsseq()
Converts simplified bed files with methylation data tobsseq
objects. -
modkit2bsseq()
Converts ONT bedmethyl files tobsseq
objects. -
pbcpg2bsseq()
Converts pb-CpG tools bedmethyl files tobsseq
objects. -
hapBSseq()
Createsbsseq
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()
InfersGRanges
objects from files or data frames, supporting various input formats.
- Update callHapDmrs function to include cpg and length parameters
- Update filterHapDmrs function
- Update documentation