Iterative Pruning to Capture Population Structure.

R Package IPCAPS

Summary

The R package IPCAPS is an unsupervised clustering algorithm based on iterative pruning to capture 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 by Intarapanich et al. (2009) <doi: 10.1186/1471-2105-10-382> and Limpiti et al. (2011)<doi: 10.1186/1471-2105-12-255>. The IPCAPS involves an iterative process using multiple splits based on multivariate Gaussian mixture modeling of principal components and Clustering EM estimation as in Lebret et al. (2015). In each iteration, rough clusters and outliers are also identified using the function rubikclust() from the R package KRIS.

The R package IPCAPS requires stats, utils, graphics, grDevices, MASS, Matrix, expm, KRIS, fpc, LPCM, apcluster, Rmixmod.

Here is the list of functions in the R package IPCAPS:

• export.groups
• get.node.info
• ipcaps
• save.eigenplots.html
• save.html
• save.plots.cluster.html
• save.plots.label.html
• save.plots
• top.discriminator

Moreover, here is the list of example datasets in the R package IPCAPS:

• label
• PC
• raw.data

Lastly, here is the list of example data files included in the directory extdata of IPCAPS:

• ipcaps_example.bed
• ipcaps_example.bim
• ipcaps_example.fam
• ipcaps_example_PC10.txt.gz
• ipcaps_example_individuals.txt.gz
• ipcapsS_example_rowVar_colInd.txt.gz
• ipcaps_example.rda

Installation

Install the released version of IPCAPS from CRAN:

install.packages("IPCAPS")

For developemenpers: problem sovling in checking the package as CRAN

Error of Roxygen2 in building RD files

The source codes in this package include the Roxgen's syntax. If there is a problem for generating the RD files (facing some errors) using RStudio (Build > Document), try to use roxygen2::roxygenise() instead of Build > Document from the menu. Alternatively, install the package devtools, then enable RStudio to use the functions from devtools (check Build > Configure Build Tools... > use devtools package functions if available) or run devtools::document() in the console.

Error of testthat for unit testing

When facing error for testthat, try to update the package testthat and add Suggests: testthat in DESCRIPTION file.

Submit package to CRAN

Check the submission using R CMD check --as-cran and a current version of r-devel, as mandated by the CRAN Repository Policy. (You could do so using the win-builder service at http://win-builder.r-project.org)

Resubmit new version to CRAN

Check downstream dependencies with devtools::revdep_check()

Error on checking DESCRIPTION meta-information in Linux

Edit ~/.profile, ~/.bash_profile or ~/.bashrc, then add

export LANG=en_US.UTF-8

export LC_ALL=en_US.UTF-8

CONTRIBUTOR CODE OF CONDUCT

As contributors and maintainers of this project, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.

We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.

Examples of unacceptable behavior by participants include the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.

Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed from the project team.

Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers.

This Code of Conduct is adapted from the Contributor Covenant, version 1.0.0, available at https://www.contributor-covenant.org/version/1/0/0/code-of-conduct.html.