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Protocols

R/qtl specifications

Information


Unique identifier OMICS_07093
Name R/qtl
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 1.42-8
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Karl W. Broman

Additional information


https://github.com/kbroman/qtl/issues http://www.rqtl.org/

Publications for R/qtl

R/qtl citations

 (555)
library_books

Mapping genetic variants for cranial vault shape in humans

2018
PLoS One
PMCID: 5919379
PMID: 29698431
DOI: 10.1371/journal.pone.0196148

[…] mative autosomal SNPs using the Illumina medium density linkage panel. Additional details regarding the genotyping and phenotyping are available [].We used Haley-Knott regression [] as implemented in R/qtl [] to identify QTLs for our phenotypes. The genome-wide significance threshold was determined using a permutation test based on 10000 replicates []. We intersected the mouse QTL results with the […]

call_split

Mapping a male fertility restoration locus for the A4 cytoplasmic genic male sterility system in pearl millet using a genotyping by sequencing based linkage map

2018
BMC Plant Biol
PMCID: 5905146
PMID: 29665794
DOI: 10.1186/s12870-018-1267-8
call_split See protocol

[…] e genome sequence, which corresponds to the numbering of the consensus map published by Rajaram et al. []. The map length was re-estimated using the Lander-Green algorithm within the software package R/qtl, and choosing the Haldane function. The genetic map with its 2343 markers contained many redundant markers (caused by co-segregation) which were excluded, thus the final linkage map was based on […]

library_books

Discovery of genomic intervals that underlie nematode responses to benzimidazoles

2018
PLoS Negl Trop Dis
PMCID: 5895046
PMID: 29601575
DOI: 10.1371/journal.pntd.0006368

[…] rcross of N2 and CB4856 [, ], as well as 153 unique C. briggsae recombinant inbred lines (RILs) created using AF16 and HK104 []. These phenotypic data were collected and processed as described above. R/qtl [] was used to carry out marker regression on 1454 C. elegans markers and 1031 C. briggsae markers. QTL were detected by calculating logarithm of odds (LOD) scores for each marker and each trait […]

library_books

A glycosyl transferase family 43 protein involved in xylan biosynthesis is associated with straw digestibility in Brachypodium distachyon

2018
New Phytol
PMCID: 5947151
PMID: 29574807
DOI: 10.1111/nph.15089

[…] releasing 35 nmol mg−1 h−1 on average.QTL analysis was conducted using the saccharification data together with SNP data for the RIL population generated by Cui et al. (). QTL analysis conducted using R/qtl (Broman & Sen, ) identified a single QTL that exceeded the LOD 5% threshold of 3.3 on chromosome 5 linked to marker BD1676_1 (Fig. a).It was calculated that this QTL accounts for 11.83% of the t […]

call_split

Biochemical and genetic analyses of N metabolism in maize testcross seedlings: 2. Roots

2018
PMCID: 5945762
PMID: 29541827
DOI: 10.1007/s00122-018-3071-0
call_split See protocol

[…] re genotyped with 5306 single nucleotide polymorphism (SNP) markers by the Beijing Genomics Institute. Physical and genetic positions of the markers were determined and genetic maps were created with R/qtl (Broman et al. ). Recombination fractions were estimated and the Kosambi mapping function was implemented to calculate genetic map distances (Kosambi ). In addition, mapping distances were adjus […]

library_books

Genetic and Developmental Basis for Increased Leaf Thickness in the Arabidopsis Cvi Ecotype

2018
Front Plant Sci
PMCID: 5861201
PMID: 29593772
DOI: 10.3389/fpls.2018.00322

[…] mentary Figure ). To determine if certain regions of the genome are associated with leaf thickness, we used publically available RIL markers to map QTL for this trait. We performed model selection in R/qtl () and decided to scan for all main effect QTL (scanone function). We reasoned that this approach could then be applied more universally (i.e., without introducing trait-specific dataset bias) t […]

Citations

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R/qtl institution(s)
Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA; Department of Horticulture, University of Wisconsin-Madison, Madison, WI, USA; Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA; 23andMe, Mountain View, CA, USA; The Jackson Laboratory, Bar Harbor, ME, USA; Department of Genetics, Genomics, and Informatics, University of Tennessee Health Sciences Center, Memphis, TN, USA; Department of Preventive Medicine, University of Tennessee Health Sciences Center, Memphis, TN, USA; Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
R/qtl funding source(s)
Supported in part by National Institutes of Health grants R01GM074244, R01GM070683, and R01GM123489.

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