Reference : IPCAPS: an R package for iterative pruning to capture population structure
Scientific journals : Article
Life sciences : Multidisciplinary, general & others
http://hdl.handle.net/2268/208622
IPCAPS: an R package for iterative pruning to capture population structure
English
Chaichoompu, Kridsadakorn [Université de Liège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Bioinformatique >]
Abegaz Yazew, Fentaw [> >]
Tongsima, Sissades [> >]
Shaw, Philip James [> >]
Sakuntabhai, Anavaj [> >]
Pereira, Luísa [> >]
Van Steen, Kristel mailto [> >]
In press
Source Code for Biology and Medicine
BioMed Central
Yes (verified by ORBi)
International
1751-0473
United Kingdom
[en] Resolving population genetic structure is challenging, especially when dealing with closely related populations. Although Principal Component Analysis (PCA)-based methods and genomic var- iation with single nucleotide polymorphisms (SNPs) are widely used to describe shared genetic an- cestry, improvements can be made targeting fine-level population structure. This work presents an R package called IPCAPS, which uses SNP information for resolving possibly fine-level population structure. The IPCAPS routines are built on the iterative pruning Principal Component Analysis (ipP- CA) framework to systematically assign individuals to genetically similar subgroups. Our tool is able to detect and eliminate outliers in each iteration to avoid misclassification. It can be extended to de- tect subtle subgrouping in patients as well. In addition, IPCAPS supports different measurement scales for variables used to identify substructure. Hence, panels of gene expression and methylation data can be accommodated.
GIGA-R Medical Genomics
Fonds de la Recherche Scientifique (Communauté française de Belgique) - F.R.S.-FNRS/ WELBIO
http://hdl.handle.net/2268/208622

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