Software for the Creation of High Density Linkage Maps in Outcrossing Species

Algorithms that build on the 'OneMap' package to create linkage maps from high density data in outcrossing species in reasonable time frames.


BatchMap is a fork of the OneMap software package for the construction of linkage maps. Specifically it aims to provide a framework that enables creating linkage maps from dense marker data (N>10,000).

Most of the non-core functionality of OneMap has been stripped and only a few functions are left at user-level. Further, this package is typically expected to be run on a headless server due to memory requirements, so all graphic functionality has also been removed.

Why use BatchMap

BatchMap employs a divide and conquer algorithm that manages to speed up the calculation of high density datasets and - additionally - scales well with higher marker numbers. It further features a routine inspired by OneMap's ripple.seq function that can adaptively reorder windows of markers to improve the order of sequences.

When not to use BatchMap

BatchMap is created specifically for F1 outcrossing populations. If your data is not that (e.g. backcross, F2, RIL), use OneMap.

Memory requirements

The twopoint table of recombination fractions and likelihoods will take 4 * 8 * N * N bytes in memory, where N is your marker number. If you have anything less than that, you need to either reduce the number of input markers, or rent a cloud server (Amazon EC2 provides high memory machines).

Installation

Install from GitHub

This will install the current development version, which is newest, but might include unstable code. If you're in doubt, install from CRAN.

install.packages("devtools")
library(devtools)
install_github("bschiffthaler/BatchMap")

Install from CRAN

This installs the latest stable version.

install.packages("BatchMap")

Note for Windows users

Windows is currently not able to parallelize R code using the parallel package. It is therefore highly recommended to use the docker container here.

Vignette - tutorial

After installation, you can read the user tutorial ('vignette') here.

Simulated experimental data is available at

Citation

This software depends whole-heartedly on the work done by all original and current authors of OneMap. We therefore ask you to cite both OneMap and BatchMap if you find BatchMap useful in your research.

News

Patch update: 1.0.1.0 This is a patch release that addresses build errors on Windows (R-oldrelease) and Solaris (all versions). Changes: - Changed identifiers in C++ sources to not start with an underscore and a - Changed std::stoul() to strtoul() from as the C++11 compiler did not support std::stoul()

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("BatchMap")

1.0.2.0 by Bastian Schiffthaler, 7 months ago


https://github.com/bschiffthaler/BatchMap


Report a bug at https://github.com/bschiffthaler/BatchMap/issues


Browse source code at https://github.com/cran/BatchMap


Authors: Bastian Schiffthaler [aut, cre], Gabriel Margarido [aut], Marcelo Mollinari [aut], Karl Broman [ctb], Augusto Garcia [aut, ctb]


Documentation:   PDF Manual  


GPL-3 license


Imports reshape2, methods

Depends on parallel, ggplot2

Suggests knitr, rmarkdown

Linking to Rcpp, RcppArmadillo


See at CRAN