Introduction to FileSetExperiment
Tim Triche, Jr.
Van Andel Institutetrichelab@gmail.com
15 August 2024
Source:vignettes/FileSetExperiment.Rmd
FileSetExperiment.RmdBasics
Install FileSetExperiment
R is an open-source statistical environment which can be easily modified to enhance its functionality via packages. FileSetExperiment is a R package available via the Bioconductor repository for packages. R can be installed on any operating system from CRAN after which you can install FileSetExperiment by using the following commands in your R session:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("FileSetExperiment")
## Check that you have a valid Bioconductor installation
BiocManager::valid()Required knowledge
FileSetExperiment is based on many other packages and in particular in those that have implemented the infrastructure needed for dealing with RNA-seq data (EDIT!). That is, packages like SummarizedExperiment (EDIT!).
If you are asking yourself the question “Where do I start using Bioconductor?” you might be interested in this blog post.
Asking for help
As package developers, we try to explain clearly how to use our packages and in which order to use the functions. But R and Bioconductor have a steep learning curve so it is critical to learn where to ask for help. The blog post quoted above mentions some but we would like to highlight the Bioconductor support site as the main resource for getting help: remember to use the FileSetExperiment tag and check the older posts. Other alternatives are available such as creating GitHub issues and tweeting. However, please note that if you want to receive help you should adhere to the posting guidelines. It is particularly critical that you provide a small reproducible example and your session information so package developers can track down the source of the error.
Citing FileSetExperiment
We hope that FileSetExperiment will be useful for your research. Please cite the package accordingly:
( add citation here; using citation causes pkgdown errors )
Reproducibility
This package was developed using biocthis.
Code for creating the vignette
## Create the vignette
library("rmarkdown")
system.time(render("FileSetExperiment.Rmd", "BiocStyle::html_document"))
## Extract the R code
library("knitr")
knit("FileSetExperiment.Rmd", tangle = TRUE)Date the vignette was generated.
# [1] "2024-08-15 17:53:15 EDT"Wallclock time spent generating the vignette.
# Time difference of 6.807 secsR session information.
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
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