FileSetExperiment

The goal of FileSetExperiment is to wrap sesame fileSet objects into a SummarizedExperiment-like object, with the corresponding expected features.

Installation instructions

Get the latest stable R release from CRAN. Then install FileSetExperiment from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("FileSetExperiment")

And the development version from GitHub with:

BiocManager::install("trichelab/FileSetExperiment")

Example

This is a basic example which shows you how to solve a common problem:

library("FileSetExperiment")
#> Loading required package: SummarizedExperiment
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#> 
#> Attaching package: 'MatrixGenerics'
#> The following objects are masked from 'package:matrixStats':
#> 
#>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#>     colWeightedMeans, colWeightedMedians, colWeightedSds,
#>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#>     rowWeightedSds, rowWeightedVars
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> 
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#> 
#>     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
#>     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
#>     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#>     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
#>     table, tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: S4Vectors
#> 
#> Attaching package: 'S4Vectors'
#> The following object is masked from 'package:utils':
#> 
#>     findMatches
#> The following objects are masked from 'package:base':
#> 
#>     expand.grid, I, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> Attaching package: 'Biobase'
#> The following object is masked from 'package:MatrixGenerics':
#> 
#>     rowMedians
#> The following objects are masked from 'package:matrixStats':
#> 
#>     anyMissing, rowMedians
#> Loading required package: sesame
#> Loading required package: sesameData
#> Loading required package: ExperimentHub
#> Loading required package: AnnotationHub
#> Loading required package: BiocFileCache
#> Loading required package: dbplyr
#> 
#> Attaching package: 'AnnotationHub'
#> The following object is masked from 'package:Biobase':
#> 
#>     cache
#> Loading sesameData.
#> 
#> ----------------------------------------------------------
#> | SEnsible Step-wise Analysis of DNA MEthylation (SeSAMe)
#> | --------------------------------------------------------
#> | Please cache auxiliary data by "sesameDataCache()".
#> | This needs to be done only once per SeSAMe installation.
#> ----------------------------------------------------------
#> Loading required package: S7

## basic example code

What is special about using README.Rmd instead of just README.md? You can include R chunks like so:

summary(cars)
#>      speed           dist       
#>  Min.   : 4.0   Min.   :  2.00  
#>  1st Qu.:12.0   1st Qu.: 26.00  
#>  Median :15.0   Median : 36.00  
#>  Mean   :15.4   Mean   : 42.98  
#>  3rd Qu.:19.0   3rd Qu.: 56.00  
#>  Max.   :25.0   Max.   :120.00

You’ll still need to render README.Rmd regularly, to keep README.md up-to-date.

You can also embed plots, for example:

In that case, don’t forget to commit and push the resulting figure files, so they display on GitHub!

Citation

Below is the citation output from using citation('FileSetExperiment') in R. Please run this yourself to check for any updates on how to cite FileSetExperiment.

print(citation("FileSetExperiment"), bibtex = TRUE)
#> To cite package 'FileSetExperiment' in publications use:
#> 
#>   trichelab (2024). _FileSetExperiment_.
#>   doi:10.18129/B9.bioc.FileSetExperiment
#>   <https://doi.org/10.18129/B9.bioc.FileSetExperiment>,
#>   https://github.com/trichelab/FileSetExperiment/FileSetExperiment - R
#>   package version 0.99.0,
#>   <http://www.bioconductor.org/packages/FileSetExperiment>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {FileSetExperiment},
#>     author = {{trichelab}},
#>     year = {2024},
#>     url = {http://www.bioconductor.org/packages/FileSetExperiment},
#>     note = {https://github.com/trichelab/FileSetExperiment/FileSetExperiment - R package version 0.99.0},
#>     doi = {10.18129/B9.bioc.FileSetExperiment},
#>   }
#> 
#>   trichelab (2024). "Analysis of large cohorts with FileSeteExperiment
#>   objects." _bioRxiv_. doi:10.1101/TODO <https://doi.org/10.1101/TODO>,
#>   <https://www.biorxiv.org/content/10.1101/TODO>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {Analysis of large cohorts with FileSeteExperiment objects},
#>     author = {{trichelab}},
#>     year = {2024},
#>     journal = {bioRxiv},
#>     doi = {10.1101/TODO},
#>     url = {https://www.biorxiv.org/content/10.1101/TODO},
#>   }

Please note that the FileSetExperiment was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the FileSetExperiment project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Development tools

• Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
• Code coverage assessment is possible thanks to codecov and covr.
• The documentation website is automatically updated thanks to pkgdown.
• The code is styled automatically thanks to styler.
• The documentation is formatted thanks to devtools and roxygen2.

For more details, check the dev directory.

This package was developed using biocthis.