msap: An R package for analyzing epigenetic and genetic diversity and differentiation in MSAP assays
The program provides a deep analysis of epigenetic variation
starting from a binary data matrix indicating the presence or
absence of EcoRI-HpaII and EcoRI-MspI
fragments, typical of MSAP technique. After comparing the data from
both enzyme combinations, the program determines if each fragment is
susceptible to methylation (representative of epigenetic variation)
or if there is no evidence of methylation (representative of genetic
variation). Different analyses of the variation (genetic and
epigenetic) among user-defined groups of samples are then performed,
as well as the classification of the methylation occurrences in
those groups. Statistical testing provide support to the analyses. A
comprehensive report of the analyses and several useful plots could
help researchers to asses the epigenetic variation in their
experiments using MSAP technique.
The package is intended to be easy to use even for those people non-familiar to the R environment. Advanced users could take advantage of available source code to adapt msap for more complex analyses.
Download and Installation
You can install msap automatically from within a R session:
- To install the last stable version from CRAN:
- To install the last daily build, execute the following command within a session in R:
install.packages("msap", repos= c("http://R-Forge.R-project.org", getOption("repos")))
Alternatively, you can download the package for local installation here.
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Dep. Bioquímica, Xenética e Inmunoloxía.
Facultade de Bioloxía. Universidade de Vigo.
36310 Vigo. Spain.
Tfn/fax: (34) 986 813828