RoAM Toolbox for Matlab®

RoAM allows reconstruction of high-resolution, genome-wide, methylation maps from high-coverage ancient DNA sequencing data. The software computes a C->T ratio for all CpGs in the genome and use these data to evaluate the genome-wide methylation, as well as to identify differentially-methylated regions (DMRs).

Core objects:

DMRs

All information on DMRs.

Processing CpG positions:

collectCpGinformation

Organizes all information on each CpG position in a single structure.

diagnose

Computes statistics on the CpG positions, and recommends filtering parameters.

filterCpGs

Decides which CpG sites should be removed.

mergeCpGs

Merges information from the two consecutive positions of each CpG.

effcoverage

Computes genome-wide CpG effective coverage.

estimatedrate

Estimates deamination rate.

estimatemodel

Combines diagnose.m and estimatedrate.m.

Computing methylation:

tOct2meth

computes methylation in each CpG position.

meanmeth

computes genome-wide mean methylation.

Supporting functions:

findlowcoveragethreshold

find threshold for removing low-coverage regions.

nanconv

NaN-aware convolution.

nanmerge

Nan-aware merger of CpG information.

nansmooth

NaN-aware smooth.

The toolbox is freely available from this site. The latest release is MVA_13Sep2010.
Prerequisite: the toolbox General Utilities.