Pvclust: an R package for assessing the uncertainty in hierarchical clustering | Zendy

Ryota Suzuki | Zendy; Hidetoshi Shimodaira | Zendy

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Pvclust: an R package for assessing the uncertainty in hierarchical clustering

Author(s) -

Ryota Suzuki,

Hidetoshi Shimodaira

Publication year - 2006

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btl117

Subject(s) - resampling , r package , computer science , cluster analysis , permutation (music) , hierarchical clustering , mit license , computation , source code , code (set theory) , data mining , software , license , cluster (spacecraft) , algorithm , statistics , mathematics , artificial intelligence , computational science , programming language , physics , acoustics , set (abstract data type) , operating system

Pvclust is an add-on package for a statistical software R to assess the uncertainty in hierarchical cluster analysis. Pvclust can be used easily for general statistical problems, such as DNA microarray analysis, to perform the bootstrap analysis of clustering, which has been popular in phylogenetic analysis. Pvclust calculates probability values (p-values) for each cluster using bootstrap resampling techniques. Two types of p-values are available: approximately unbiased (AU) p-value and bootstrap probability (BP) value. Multiscale bootstrap resampling is used for the calculation of AU p-value, which has superiority in bias over BP value calculated by the ordinary bootstrap resampling. In addition the computation time can be enormously decreased with parallel computing option.

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