PCAdmix statistics

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PCAdmix specifications

Information


Unique identifier OMICS_25962
Name PCAdmix
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages R
License MIT License
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Abra Brisbin <>
  • person_outline Carlos Bustamante <>

Publication for PCAdmix

PCAdmix in publications

 (23)
PMCID: 5834599
PMID: 29500350
DOI: 10.1038/s41467-018-03342-5

[…] 25, --window-size 0.01; --min-node-size 5. finally, the second dataset (with a focus on southeast asia and east african source populations) was analyzed; the data were phased with shapeit and pcadmix was used to evaluate local ancestry., furthermore, as an independent test, we used an unsupervised global ancestry method to perform the estimation and the magnitude of deviations across […]

PMCID: 5727231
PMID: 29233967
DOI: 10.1038/s41467-017-00663-9

[…] with geography that could be due to variation in levels of bantu-speaking admixture in the ks populations (e.g., the khwe). to reduce bias on the fst estimates introduced due to admixture, we used pcadmix to identify and mask genomic regions with non-niger-congo (nc) ancestry and repeated the analysis, (supplementary note ). the results showed the estimates from using the genomic regions […]

PMCID: 5548776
PMID: 28790322
DOI: 10.1038/s41598-017-07382-7

[…] b and c that surpasses that between a and c and/or b and d. to determine extreme f3/f4 values, a data normalisation and outlier detection approach was implemented (see supplementary text )., we used pcadmix v1.0 to infer local genomic ancestry. pcadmix utilises haplotypes from ancestral representatives to infer ancestry of focal individuals. the software performs the inference chromosome-wide […]

PMCID: 5850710
PMID: 28549194
DOI: 10.1093/molbev/msx169

[…] dogs in the hyb samples (z-score = −72.064). to better estimate the actual admixture proportions in the analyzed hybrids (), we applied a pca-based admixture deconvolution approach implemented in pcadmix (), which identified 1.2–51.6% dog blocks in the genome of the hybrid individuals. these proportions highly correlated with those estimated in admixture at k = 2 (r2 = 0.969; p < 0.01), […]

PMCID: 5510585
PMID: 28717592
DOI: 10.7717/peerj.3522

[…] shapeit (), we constructed a genetic map file as the ratio of inter-snp distances to the position of the last snp queried on chromosome 10. additionally, we phased snp genotypes using the program pcadmix and plotted the per-individual loadings for the first two coordinates (). lastly, we applied a haplotype-based test (; ) to determine if the shared epas1 haplotype in highland dogs and wolves […]


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PCAdmix institution(s)
Department of Biostatistics and Computational Biology, Cornell University, Ithaca, NY, USA; Department of Genetics, Stanford University, Stanford, CA, USA; Department of Pathology and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
PCAdmix funding source(s)
Supported by NSF grant number 0516310.

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