# Methylation array and sequencing spatial analysis methods

## Documentation for package ‘DMRcate’ version 3.5.2

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

## Help Pages

DMRcate-package | DMR calling from bisulfite sequencing and Illumina array data
changeFDR | Change the individual CpG FDR thresholding for a CpGannotated object.
cpg.annotate | Annotate Illumina CpGs with their chromosome position and test statistic
CpGannotated-class | An object summarising individual CpG sites fitted to a given model
DMR.plot | Plotting DMRs
DMRcate | DMR calling from bisulfite sequencing and Illumina array data
dmrcate | DMR identification
DMResults-class | Initial storage object for called DMRs - class
extractRanges | Create a GRanges object from 'dmrcate' output.
getCollapsedBetas | Extract a beta matrix from a CpGannotated object.
plot | Plotting DMRs
rmSNPandCH | Filter probes
sequencing.annotate | Annotate a bisulfite sequencing experiment (WGBS or RRBS) with probe weights and chromosomal position.