DAMEfinder {DAMEfinder} | R Documentation

## DAMEfinder: Method to detect allele-specific methylation (ASM), and differential ASM from Bisulfite sequencing data in R.

### Description

The package allows the user to extract an ASM score in two ways: either from a `bismark` bam file(s) and VCF file(s), or from the output from `methtuple`. Either way the final output is a list of regions with diferential allele-specific methylated between groups of samples of interest. The package also provides functions to visualize ASM at the read level or the score level

### DAMEfinder functions

`calc_asm` extracts ASM for pairs of CpG sites from a methtuple file, `calc_derivedasm` extracts ASM at each CpG site linked to a SNP from the VCF file. Both functions generate a `RangedSummarizedExperiment`, which is the input for the main function `find_dames`, that generates a `data.frame` with regions exhibiting differential ASM between a number of samples.

### Author(s)

Stephany Orjuela sorjuela@gmail.com

Dania Machlab

Mark D Robinson mark.robinson@imls.uzh.ch

[Package DAMEfinder version 0.99.4 Index]