# Finds DAMEs - Differential Allelicly MEthylated regions

## Documentation for package ‘DAMEfinder’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

calc_asm | Calculate ASM Score
calc_derivedasm | Calculate SNP-based ASM
calc_logodds | Calculate the log odds ratio
calc_score | Calculate score
calc_weight | Calculate Weight for ASM Score
DAMEfinder | DAMEfinder: Method to detect allele-specific methylation (ASM), and differential ASM from Bisulfite sequencing data in R.
dame_track | Plot score tracks
dame_track_mean | Plot means per group of score tracks.
extractbams_output | extract_bams() output.
extract_bams | Detect allele-specific methylation from a bam file
find_dames | Find DAMEs
get_tstats | Get t-Statistics
methyl_circle_plot | Draw methylation circle plot
methyl_circle_plotCpG | Draw methylation circle plot without SNP
methyl_MDS_plot | Multidimensional scaling plot of distances between methylation proportions (beta values)
modulus_sqrt | Get Modulus Square Root
readtuples_output | read_tuples() output.
read_tuples | Read in list of methtuple files