R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis

Julian Taylor and David Butler

Journal of Statistical Software, 2017, vol. 079, issue i06

Abstract: Although various forms of linkage map construction software are widely available, there is a distinct lack of packages for use in the R statistical computing environment (R Core Team 2017). This article introduces the ASMap linkage map construction R package which contains functions that use the efficient MSTmap algorithm (Wu, Bhat, Close, and Lonardi 2008) for clustering and optimally ordering large sets of markers. Additional to the construction functions, the package also contains a suite of tools to assist in the rapid diagnosis and repair of a constructed linkage map. The package functions can also be used for post linkage map construction techniques such as fine mapping or combining maps of the same population. To showcase the efficiency and functionality of ASMap, the complete linkage map construction process is demonstrated with a high density barley backcross marker data set.

Date: 2017-07-13
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.jstatsoft.org/index.php/jss/article/view/v079i06/v79i06.pdf
https://www.jstatsoft.org/index.php/jss/article/do ... 6/ASMap_1.0-0.tar.gz
https://www.jstatsoft.org/index.php/jss/article/do ... ile/v079i06/v79i06.R
https://www.jstatsoft.org/index.php/jss/article/do ... 079i06/ASMap_funcs.R

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:jss:jstsof:v:079:i06

DOI: 10.18637/jss.v079.i06

Access Statistics for this article

Journal of Statistical Software is currently edited by Bettina Grün, Edzer Pebesma and Achim Zeileis

More articles in Journal of Statistical Software from Foundation for Open Access Statistics
Bibliographic data for series maintained by Christopher F. Baum ().