A paragraph that describes the purpose of the package. Explain how your package add to or improve a current work flow in bioinformatics or computational biology (i.e., how is it unique?, what issue does it address?).
E.g., TestingPackage is an R package to demonstrate components of a
simple R package. This includes the main components: DESCRIPTION,
NAMESPACE, man subdirectory and R subdirectory. Additionally, licence,
README and subdirectories vignettes, tests, data and inst are also
explored. The package is targeted for BCB410H students exploring
development of an R package in bioinformatics.
To install the latest version of the package:
require("devtools")
devtools::install_github("anjalisilva/TestingPackage", build_vignettes = TRUE)
library("TestingPackage")To run the Shiny app:
runTestingPackage()ls("package:TestingPackage")
data(package = "TestingPackage") # optionalAfter these commands, provide an overview that briefly describes the main components of the package. Point the user to vignettes for more details. Include an image illustrating the overview of the package.
E.g., TestingPackage contains 4 functions to demonstrate components of
a simple R package. The InfCriteriaCalculation function calculates the
information criteria values. Specifically, Bayesian information
criterion (BIC), Akaike information criterion (AIC) and Integrated
Complete Likelihood (ICL) are calculated. The InfCriteriaPlot
generates a plot of information criteria values. NormFactors is a
function that calculates normalization factors via Trimmed Mean of
M-values (TMM). The runTestingPackage is the function that launches
the shiny app for this package. The package also contains RNA sequencing
dataset GeneCounts. Refer to package vignettes for more details.
browseVignettes("TestingPackage")The package tree structure is provided below (optional).
- TestingPackage
|- TestingPackage.Rproj
|- DESCRIPTION
|- NAMESPACE
|- LICENSE
|- README
|- data
|- GeneCounts.rda
|- inst
CITATION
|- extdata
|- SILVA_A_A1.png
|- shiny-scripts
|- app.R
|- man
|- GeneCounts.Rd
|- InfCriteriaCalculation.Rd
|- NormFactors.Rd
|- InfCriteriaPlot.Rd
|- R
|- data.R
|- InfCriteriaCalculation.R
|- InfCriteriaPlot.R
|- NormFactorCalculation.R
|- vignettes
|- TestingPackageVignette.Rmd
|- tests
|- testthat.R
|- testthat
|- test-InfCriteriaCalculation.RAn overview of the package is illustrated below.
Provide a note clearly indicating contributions from you and contributions from other packages/sources for each function. Remember your individual contributions to the package are important.
E.g., The author of the package is Anjali Silva. The
InfCriteriaCalculation function makes use of map function from
mclust R package to generate ICL values. The stats R package is used
for generating multinomially distributed random number vectors. (If
applies: Part of the code for InfCriteriaCalculation function has been
taken from <NamePackage> R package. Section of the borrowed code is
clearly indicated and referenced in the InfCriteriaCalculation help
file). The InfCriteriaPlot makes use of the graphics R package.
NormFactors uses Trimmed Mean of M-values (TMM) as implemented in
edgeR R package.
Provide full references for all sources used in one specific format. E.g.,
Akaike, H. (1973). Information theory and an extension of the maximum likelihood principle. In Second International Symposium on Information Theory, New York, NY, USA, pp. 267–281. Springer Verlag. https://link.springer.com/chapter/10.1007/978-1-4612-1694-0_15.
Biernacki, C., G. Celeux, and G. Govaert (2000). Assessing a mixture model for clustering with the integrated classification likelihood. IEEE Transactions on Pattern Analysis and Machine Intelligence 22. https://hal.inria.fr/inria-00073163/document
BioRender. (2020). Image created by Silva, A. Retrieved October 30, 2020, from https://app.biorender.com/
R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/
Schwarz, G. (1978). Estimating the dimension of a model. The Annals of Statistics 6, 461–464. https://projecteuclid.org/euclid.aos/1176344136.
Wickham, H. and Bryan, J. (2019). R Packages (2nd edition). Newton, Massachusetts: O’Reilly Media. https://r-pkgs.org/
This package was developed for BCB410H: Applied Bioinformatics,
University of Toronto, Toronto, CANADA, 2019-2021. TestingPackage
welcomes issues, enhancement requests, and other contributions. To
submit an issue, use the GitHub
issues.
Packages developed by BCB410 students: