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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

Versioning


No version available

Maintainers


  • person_outline Abra Brisbin
  • person_outline Carlos Bustamante

Publication for PCAdmix

PCAdmix citations

 (26)
library_books

Strong selection during the last millennium for African ancestry in the admixed population of Madagascar

2018
Nat Commun
PMCID: 5834599
PMID: 29500350
DOI: 10.1038/s41467-018-03342-5

[…] rations 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 the gen […]

call_split

The Gateway from Near into Remote Oceania: New Insights from Genome Wide Data

2018
Mol Biol Evol
PMCID: 5889034
PMID: 29301001
DOI: 10.1093/molbev/msx333
call_split See protocol

[…] To infer local ancestry along individual chromosomes and obtain the genome-wide block-like signal of admixture we used a PCA-based approach implemented in the PCAdmix software (). In choosing the proxies which would best represent the parental populations we followed the results of the 3-population test and ADMIXTURE analyses. Specifically, we used the PNG […]

library_books

Whole genome sequencing for an enhanced understanding of genetic variation among South Africans

2017
Nat Commun
PMCID: 5727231
PMID: 29233967
DOI: 10.1038/s41467-017-00663-9

[…] typed on the Illumina Omni 2.5 M SNP chip—were merged together using PLINK v1.9. The merged data set was phased using SHAPEIT2 with standard parameters. Analysis of local ancestry was performed using PCAdmix, with Ju/’hoansi, YRI, and non-African (CEU, CHB, and JPT) as the three ancestral populations and the SEB2 from Schlebusch et al. as the target population). Based on the ascertainment of ances […]

library_books

Autosomal and Mitochondrial Adaptation Following Admixture: A Case Study on the Honeybees of Reunion Island

2017
Genome Biol Evol
PMCID: 5814903
PMID: 29202174
DOI: 10.1093/gbe/evx247

[…] o investigate whether or not the distribution of the principal genetic backgrounds identified (A. m. unicolor and C lineage) in the Reunion population was heterogenous, the data were preprocessed for PCAdmix () and Chromosomal Ancestry Differences (CAnD) analyses (). The initial 3.7-M SNP data were first filtered to retain only samples from Reunion, together with the haploid A. m. carnica, A. m. l […]

library_books

Genomic signatures of adaptive introgression from European mouflon into domestic sheep

2017
Sci Rep
PMCID: 5548776
PMID: 28790322
DOI: 10.1038/s41598-017-07382-7

[…]  < 0.95) than domestic sheep (~12%).PCAdmix therefore provided estimates of genome-wide admixture proportions for mouflon and domestic sheep that were consistent with results from Admixture. However, PCAdmix results for particular genomic regions – the main goal of using this approach - showed inconsistency with regard to the location and length of inferred admixture regions (Fig. , Supplementary […]

library_books

Disentangling Timing of Admixture, Patterns of Introgression, and Phenotypic Indicators in a Hybridizing Wolf Population

2017
Mol Biol Evol
PMCID: 5850710
PMID: 28549194
DOI: 10.1093/molbev/msx169

[…] ses (see results). Individual assignment values of hybrids were verified running again the software using the “supervised approach”, which allows to fix the reference populations (), and confirmed by PCAdmix (; see below), which is more appropriate in evaluating the actual admixture proportions (). We used the f3 test in ThreePop (TreeMix package 1.12; ) to formally assess the occurrence of admixt […]

Citations

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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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