IPCAPS: an R package for iterative pruning to capture population structure View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-12

AUTHORS

Kridsadakorn Chaichoompu, Fentaw Abegaz, Sissades Tongsima, Philip James Shaw, Anavaj Sakuntabhai, Luísa Pereira, Kristel Van Steen

ABSTRACT

Background: Resolving population genetic structure is challenging, especially when dealing with closely related or geographically confined populations. Although Principal Component Analysis (PCA)-based methods and genomic variation with single nucleotide polymorphisms (SNPs) are widely used to describe shared genetic ancestry, improvements can be made especially when fine-scale population structure is the target. Results: This work presents an R package called IPCAPS, which uses SNP information for resolving possibly fine-scale population structure. The IPCAPS routines are built on the iterative pruning Principal Component Analysis (ipPCA) framework that systematically assigns individuals to genetically similar subgroups. In each iteration, our tool is able to detect and eliminate outliers, hereby avoiding severe misclassification errors. Conclusions: IPCAPS supports different measurement scales for variables used to identify substructure. Hence, panels of gene expression and methylation data can be accommodated as well. The tool can also be applied in patient sub-phenotyping contexts. IPCAPS is developed in R and is freely available from http://bio3.giga.ulg.ac.be/ipcaps. More... »

PAGES

2

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13029-019-0072-6

DOI

http://dx.doi.org/10.1186/s13029-019-0072-6

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1112895378

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30936940


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