GWASpoly statistics

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GWASpoly specifications

Information


Unique identifier OMICS_25063
Name GWASpoly
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
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Jeffrey Endelman <>

Publication for GWASpoly

GWASpoly in publications

 (3)
PMCID: 5915555
PMID: 29720992
DOI: 10.3389/fpls.2018.00513

[…] define a relatedness metric between polyploid individuals (i.e., how to generate the kinship matrix, k). so far, there have been two software tools released for polyploid gwas, namely the r package gwaspoly () and the previously mentioned shesisplus (). of these, only gwaspoly looks critically at the form of the kinship matrix k. three different forms of k were tested in the development […]

PMCID: 5945755
PMID: 29470621
DOI: 10.1007/s00122-018-3073-y

[…] wheat accessions were used to identify marker–trait associations using mixed linear model (mlms) analyses accounting for the population structure and kinship as fixed effects using the package gwaspoly in r (rosyara et al. ). to identify snp/dart markers with significant associations, two thresholds were applied for different phenotyping methods. for the effector-sensitivity assay […]

PMCID: 5336250
PMID: 28257509
DOI: 10.1371/journal.pone.0173039

[…] of andigena accessions were used to identify marker-trait association using mixed linear model (mlms) analyses accounting for the population structure and kinship as fixed effects using the package gwaspoly [] in the r software []. additionally, the andigena genotypic data was filtered with the default parameters of gwaspoly [] (5% of missing data and a maf of 0.10). to identify the snps […]


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GWASpoly institution(s)
Department of Horticulture, University of Wisconsin, Madison, WI, USA; School of Integrative Plant Science, Cornell University, Ithaca, NY, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
GWASpoly funding source(s)
Supported by USDA-NIFA-SCRI Grant No. 2011-51181-30629 (Improved Breeding and Variety Evaluation Methods to Reduce Acrylamide Content and Increase Quality in Processed Potato Products), USDA-NIFA-Hatch Accession No. 1002731 (Genome-wide Association Analysis and Breeding in Potato).

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