In kridsadakorn/ipcaps.bioc: Iterative Pruning to Capture Population Structure

knitr::opts_chunk$set(echo = TRUE)

R Package IPCAPS.BIOC

Summary

The R package IPCAPS.BIOC 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 (Intarapanich et al., 2009; Limpiti et al., 2011). The IPCAPS.BIOC 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.BIOC requires stats, utils, graphics, grDevices, MASS, Matrix, expm, KRIS, fpc, LPCM, apcluster, Rmixmod, doMC, foreach, parallel.

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

• 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.BIOC:

• label
• raw.data
• snp.info
• ind.info
• PC

The example datasets can be loaded by:

data(ipcaps_example)

Except for "PC", it can be loaded by:

data(ipcaps_example_PC10)

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

• ipcaps_example.bed
• ipcaps_example.bim
• ipcaps_example.fam
• ipcaps_example.RData
• ipcaps_example_PC10.RData
• ipcaps_example_PC10.txt.gz
• ipcaps_example_individuals.txt.gz
• ipcaps_example_rowVar_colInd.txt.gz

Installation

Install the developing version of IPCAPS.BIOC from GitHub:

devtools::install_github("kridsadakorn/ipcaps.bioc")

Load the package

To load the package, use this command:

library(IPCAPS.BIOC)

Quick start

Check the vignettes in the packages:

• Supported input formats
• How to analyze SNP data

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.

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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

kridsadakorn/ipcaps.bioc documentation built on Jan. 22, 2020, 11:18 p.m.