Keen and Reliable Interface Subroutines for Bioinformatic Analysis

Provides useful functions which are needed for bioinformatic analysis such as calculating linear principal components from numeric data and Single-nucleotide polymorphism (SNP) dataset, calculating fixation index (Fst) using Hudson method, creating scatter plots in 3 views, handling with PLINK binary file format, detecting rough structures and outliers using unsupervised clustering, and calculating matrix multiplication in the faster way for big data.



title: "README" author: "Kridsadakorn Chaichoompu" date: "04/06/2018" output: html_document: keep_md: yes toc: yes pdf_document: number_sections: yes toc: yes

Summary

The R package KRIS (Keen and Reliable Interface Subroutines for bioinformatic analysis) is the package providing useful functions which are needed for bioinformatic analysis such as calculating linear principal components from numeric data and Single-nucleotide polymorphism (SNP) dataset, calculating fixation index (Fst) using Hudson method, creating scatter plots in 3 views, handling with PLINK binary file format, detecting rough structures and outliers using unsupervised clustering, and calculating matrix multiplication in the faster way for big data.

The R package KRIS requires the package rARPACK.

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

  • cal.pc.linear
  • cal.pc.projection
  • fst.each.snp.hudson
  • fst.hudson
  • plot3views
  • read.bed
  • rubikclust
  • write.bed
  • xxt

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

  • simsnp
  • sample_labels

Installation

Install the released version of KRIS from CRAN:

install.packages("KRIS")

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

News


title: "NEWS" author: "Kridsadakorn Chaichoompu" date: "04/06/2018" output: html_document: keep_md: yes toc: yes pdf_document: number_sections: yes toc: yes

KRIS 1.1.1

Updates

  • Updated and added more examples in plot3view

KRIS 1.1.0

New features

  • Added the function cal.pc.projection

Updates

  • Moved replace.missing to for_parallel.R from principal.component.R

Fixed bugs

  • Fixed bugs in test_plot3views.R

KRIS 1.0.4

Updates

  • Changed URL in the CITATION file from Gitlab to CRAN
  • Changed email in the DESCRIPTION file from Gmail to Official email
  • Fixed misspelling in a manual of data

KRIS 1.0.3

Updates

  • Updated URLs and added details of package in the DESCRIPTION file
  • Updated manual of all functions according from CRAN's comments

KRIS 1.0.2

Updates

  • Fixed the help file for read.bed, read.bed, fst.each.snp.hudson and fst.hudson.

KRIS 1.0.1

Updates

  • Fixed the help file for cal.pc.linear and rubikclust.

KRIS 1.0.0.0

Initial functions

  • cal.pc.linear A function for linear principal component analysis (PCA)
  • fst.each.snp.hudson A function for fixation index (Fst) calculation for all SNPs between two groups.
  • fst.hudson A function for average fixation index (Fst) calculation between two groups.
  • plot3views A function to create scatter plots in three views.
  • read.bed Read the binary PLINK format (BED, BIM, and FAM)
  • rubikclust A function for unsupervised clustering to detect rough structures and outliers.
  • write.bed Write an list of SNP object to the binary PLINK format (BED, BIM, and FAM)
  • xxt A function for calculating matrix multipication between a matrix and its transpose for large data.

Initial R data

  • simsnp Synthetic dataset containing single nucleotide polymorphisms (SNP)
  • sample_labels Synthetic dataset containing population labels for the dataset simsnp.

Initial example files

  • example_SNP.bed Synthetic dataset containing single nucleotide polymorphisms (SNP) in binary format
  • example_SNP.bim Simulated SNP information
  • example_SNP.fam Simulated sample information

Updates

From the initial idea, some functions were changed their names:

  • The name of function cal.PC.linear was changed to cal.pc.linear.
  • The name of function plot.3views was changed to plot3views.
  • The name of function rubikClust was changed to rubikclust.
  • The name of function XXt was changed to xxt.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("KRIS")

1.1.1 by Kridsadakorn Chaichoompu, 9 months ago


https://gitlab.com/kris.ccp/kris


Report a bug at https://gitlab.com/kris.ccp/kris/issues


Browse source code at https://github.com/cran/KRIS


Authors: Kridsadakorn Chaichoompu [aut, cre] , Kristel Van Steen [aut] , Fentaw Abegaz [aut] , Sissades Tongsima [aut] , Philip James Shaw [aut] , Anavaj Sakuntabhai [aut] , Luisa Pereira [aut]


Documentation:   PDF Manual  


GPL-2 | GPL-3 license


Imports rARPACK, grDevices, graphics, stats, utils

Suggests testthat


Imported by FILEST, IPCAPS.


See at CRAN