Fine-Level Structure Simulator.
R Package FILEST
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
create.template.setting
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
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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.