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© Research
Publication : Source code for biology and medicine

IPCAPS: an R package for iterative pruning to capture population structure.

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Source code for biology and medicine - 01 Jan 2019

Chaichoompu K, Abegaz F, Tongsima S, Shaw PJ, Sakuntabhai A, Pereira L, Van Steen K,

Link to Pubmed [PMID] – 30936940

Link to DOI [DOI] – 10.1186/s13029-019-0072-6

Source Code Biol Med 2019 ; 14(): 2

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.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.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.

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