Package: IPCAPS
Type: Package
Title: Iterative Pruning to Capture Population Structure
Version: 1.1.5
Authors@R: c(person(given = "Kridsadakorn", family = "Chaichoompu", email = "kridsadakorn@biostatgen.org", role = c("aut", "cre")), person(given = "Kristel", family = 'Van Steen', role = "aut"), person(given = "Fentaw", family = "Abegaz", role = "aut"), person(given = "Sissades", family = "Tongsima", role = "aut"), person(given = "Philip", family = "Shaw", role = "aut"), person(given = "Anavaj", family = "Sakuntabhai", role = "aut"), person(given = "Luisa", family = "Pereira", role = "aut"))
Description: An unsupervised clustering algorithm based on iterative pruning is for capturing population structure. This version supports ordinal data which can be applied directly to SNP data to identify fine-level population structure and it is built on the iterative pruning Principal Component Analysis ('ipPCA') algorithm as explained in Intarapanich et al. (2009) <doi:10.1186/1471-2105-10-382>. The 'IPCAPS' involves an iterative process using multiple splits based on multivariate Gaussian mixture modeling of principal components and 'Expectation-Maximization' clustering as explained in Lebret et al. (2015) <doi:10.18637/jss.v067.i06>. In each iteration, rough clusters and outliers are also identified using the function rubikclust() from the R package 'KRIS'.
Depends: R (>= 3.2.4.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports:
        stats,utils,graphics,grDevices,MASS,Matrix,expm,KRIS,fpc,LPCM,apcluster,Rmixmod
Suggests: testthat
BugReports: https://gitlab.com/kris.ccp/ipcaps/issues
URL: https://gitlab.com/kris.ccp/ipcaps
Collate: 'parallelization.R' 'check.stopping.R' 'clustering.mode.R'
        'clustering.R' 'data.R' 'export.groups.R' 'get.node.info.R'
        'ipcaps-package.R' 'process.each.node.R' 'output.template.R'
        'save.html.R' 'save.eigenplots.html.R'
        'save.plots.label.html.R' 'save.plots.cluster.html.R'
        'save.plots.R' 'postprocess.R' 'preprocess.R' 'ipcaps.R'
        'top.discriminator.R'
NeedsCompilation: no
Packaged: 2018-06-11 13:05:39 UTC; kridsadakorn
Author: Kridsadakorn Chaichoompu [aut, cre],
  Kristel Van Steen [aut],
  Fentaw Abegaz [aut],
  Sissades Tongsima [aut],
  Philip Shaw [aut],
  Anavaj Sakuntabhai [aut],
  Luisa Pereira [aut]
Maintainer: Kridsadakorn Chaichoompu <kridsadakorn@biostatgen.org>
Repository: CRAN
Date/Publication: 2018-06-14 18:01:51 UTC
Built: R 3.5.0; ; 2018-06-15 11:05:42 UTC; unix
