MaMaMIA (Max Mapping for Meticulous Introgression Analysis) detects interspecific introgressions from Genotyping-by-Sequencing (GBS) coverage data.
It builds a Read Count Array (RCA) from windowed donor and recipient coverage and GC-content tables, corrects GC bias with a zero-inflated negative binomial model, and segments pairwise coverage differences with circular binary segmentation (CBS) into an Introgression Segment Array (ISA). Putative introgressions can be plotted, filtered, and exported as BEDPE.
MaMaMIA ships with an example wheat dataset (triticum: T. timopheevii donor vs T. aestivum Chinese Spring T2T recipient). See vignette("Overview", package = "MaMaMIA") for a full walkthrough.
You can install MaMaMIA from GitHub with:
# install.packages("devtools")
devtools::install_github("alermol/mamamia")This package is still under active development, the content is therefore subject to change.
Suggestions and bug reports: please open an issue.