TY - JOUR T1 - IPCAPS: an R package for iterative pruning to capture population structure JF - bioRxiv DO - 10.1101/186874 SP - 186874 AU - Kridsadakorn Chaichoompu AU - Fentaw Abegaz Yazew AU - Sissades Tongsima AU - Philip James Shaw AU - Anavaj Sakuntabhai AU - LuĂ­sa Pereira AU - Kristel Van Steen Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/09/10/186874.abstract N2 - 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 bio3.giga.ulg.ac.be/ipcapsFSTfixation indexLDlinkage disequilibriumPCprincipal componentPCAprincipal component analysisQCquality controlSNPsingle nucleotide polymorphisms ER -