Fine-Level Structure Simulator

A population genetic simulator, which is able to generate synthetic datasets for single-nucleotide polymorphisms (SNP) for multiple populations. The genetic distances among populations can be set according to the Fixation Index (Fst) as explained in Balding and Nichols (1995) . This tool is able to simulate outlying individuals and missing SNPs can be specified. For Genome-wide association study (GWAS), disease status can be set in desired level according risk ratio.



title: "README" author: "Kridsadakorn Chaichoompu" date: "07/06/2018" output: html_document: keep_md: yes toc: yes pdf_document: number_sections: yes toc: yes

Summary

The R package FILEST (Fine-Level Structure Simulator) is a population genetic simulator. The simulator is able to generate synthetic datasets for single-nucleotide polymorphisms (SNP) for multiple populations. The genetic distances among populations can be set according to the Fixation Index (Fst). This tool is able to simulate outlying individuals and missing SNPs can be specified. For Genome-wide association study (GWAS), disease status can be set in desired level according risk ratio.

The R package FILEST requires KRIS and rARPACK

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

  • cbind_bigmatrix
  • demo.filest
  • filest
  • rbind_bigmatrix

Installation

Install the released version of FILEST from CRAN:

install.packages("FILEST")

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: "07/06/2018" output: html_document: keep_md: yes toc: yes pdf_document: number_sections: yes toc: yes

FILEST 1.0.2

Updates

  • Added references in the DESCRIPTION file
  • Added single quotes for Software's names in the DESCRRIPTION file
  • Added checking for output directory and input file

FILEST 1.0.1

Updates

  • FILEST 1.0.1 is released under GPL-2|GPL-3

FILEST 1.0.0

NOTES

  • Shift from 0.3.7 to 1.0.0 to release

Updates

  • Romoved all codes related to doMC and doParallel, there is a problem in Windows.

FILEST 0.3.7

Updates

  • Added all manual files for all functions
  • Added all unit tests

Changes

  • Removed save.PC.plot() and replaced with KRIS::plot3views

FILEST 0.3.6

Initial project in GitLab

  • Uploaded and Synchronized all files

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("FILEST")

1.0.3 by Kridsadakorn Chaichoompu, 8 months ago


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


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


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


Authors: Kridsadakorn Chaichoompu [aut, cre] , Kristel Van Steen [aut] , Fentaw Abegaz [aut]


Documentation:   PDF Manual  


GPL-2 | GPL-3 license


Imports KRIS, rARPACK, grDevices, stats, utils

Suggests testthat


See at CRAN