ArticlePloS one2019
Consequences of PCA graphs, SNP codings, and PCA variants for elucidating population structure.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed.
- Linking root length and surface area to yield: variety-specific root plasticity in winter wheat across contrasting European environments.Annals of botany · 2025Article
- Maximizing the accuracy of genetic variance estimation and using a novel generalized effective sample size to improve simulations.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Genomic analysis reveals low genetic diversity and no continuous reintroduction of piscine myocarditis virus in farmed Atlantic salmon in the Faroe Islands.The Journal of general virology · 2025Article
- Genome-Wide Association Analysis of Freezing Tolerance and Winter Hardiness in Winter Wheat of Nordic Origin.Plants (Basel, Switzerland) · 2023Article
- Contrastive multiple correspondence analysis (cMCA): Using contrastive learning to identify latent subgroups in political parties.PloS one · 2023Article
- Article
- Population structure and genetic diversity of the Pee Dee cotton breeding program.G3 (Bethesda, Md.) · 2021Article
- Evaluation of variant calling tools for large plant genome re-sequencing.BMC bioinformatics · 2020Article
- Genome-wide association mapping of Fusarium langsethiae infection and mycotoxin accumulation in oat (Avena sativa L.).The plant genome · 2020Article
- Resistance Mechanisms ofG3 (Bethesda, Md.) · 2020Article
- Marginal diversity analysis of conservation of Chinese domestic duck breeds.Scientific reports · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
SNP datasets are high-dimensional, often with thousands to millions of SNPs and hundreds to thousands of samples or individuals. Accordingly, PCA graphs are frequently used to provide a low-dimensional visualization in order to display and discover patterns in SNP data from humans, animals, plants, and microbes-especially to elucidate population structure. PCA is not a single method that is always done the same way, but rather requires three choices which we explore as a three-way factorial: two kinds of PCA graphs by three SNP codings by six PCA variants. Our main three recommendations are simple and easily implemented: Use PCA biplots, SNP coding 1 for the rare allele and 0 for the common allele, and double-centered PCA (or AMMI1 if main effects are also of interest). We also document contemporary practices by a literature survey of 125 representative articles that apply PCA to SNP data, find that virtually none implement our recommendations. The ultimate benefit from informed and optimal choices of PCA graph, SNP coding, and PCA variant, is expected to be discovery of more biology, and thereby acceleration of medical, agricultural, and other vital applications.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.