Ronald M Nelson1, Xia Shen, Orjan Carlborg. 1. Department of Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-75007 Uppsala, Sweden. Ronnie.Nelson@slu.se.
Abstract
BACKGROUND: qtl.outbred is an extendible interface in the statistical environment, R, for combining quantitative trait loci (QTL) mapping tools. It is built as an umbrella package that enables outbred genotype probabilities to be calculated and/or imported into the software package R/qtl. FINDINGS: Using qtl.outbred, the genotype probabilities from outbred line cross data can be calculated by interfacing with a new and efficient algorithm developed for analyzing arbitrarily large datasets (included in the package) or imported from other sources such as the web-based tool, GridQTL. CONCLUSION: qtl.outbred will improve the speed for calculating probabilities and the ability to analyse large future datasets. This package enables the user to analyse outbred line cross data accurately, but with similar effort than inbred line cross data.
BACKGROUND: qtl.outbred is an extendible interface in the statistical environment, R, for combining quantitative trait loci (QTL) mapping tools. It is built as an umbrella package that enables outbred genotype probabilities to be calculated and/or imported into the software package R/qtl. FINDINGS: Using qtl.outbred, the genotype probabilities from outbred line cross data can be calculated by interfacing with a new and efficient algorithm developed for analyzing arbitrarily large datasets (included in the package) or imported from other sources such as the web-based tool, GridQTL. CONCLUSION: qtl.outbred will improve the speed for calculating probabilities and the ability to analyse large future datasets. This package enables the user to analyse outbred line cross data accurately, but with similar effort than inbred line cross data.
Authors: Henrike O Heyne; Susann Lautenschläger; Ronald Nelson; François Besnier; Maxime Rotival; Alexander Cagan; Rimma Kozhemyakina; Irina Z Plyusnina; Lyudmila Trut; Örjan Carlborg; Enrico Petretto; Leonid Kruglyak; Svante Pääbo; Torsten Schöneberg; Frank W Albert Journal: Genetics Date: 2014-09-03 Impact factor: 4.562
Authors: Ronald M Nelson; Carl Nettelblad; Mats E Pettersson; Xia Shen; Lucy Crooks; Francois Besnier; José M Alvarez-Castro; Lars Rönnegård; Weronica Ek; Zheya Sheng; Marcin Kierczak; Sverker Holmgren; Orjan Carlborg Journal: G3 (Bethesda) Date: 2013-12-09 Impact factor: 3.154