BiocIO contains defintions for import and export methods used throughout Biocondcutor for IO purposes. The BiocFile class which serves as an interface for File classes within Bioconductor is also defined in this package. This vignette will describe the functionality of these base methods and classes as well as an example for developers on how to interface with them.
BiocIO 1.14.0
The BiocIO package is primarily to be used by developers for interfacing with
the abstract classes and generics in this package to develop their own related
classes and methods.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BiocIO")library("BiocIO")The functions import and export load and save objects from and to particular file formats. This package contains the following generics for the import and export methods used throughout the Bioconductor package suite.
getGeneric("import")## standardGeneric for "import" defined from package "BiocIO"
##
## function (con, format, text, ...)
## standardGeneric("import")
## <bytecode: 0x55d63d57c818>
## <environment: 0x55d63d52dbe8>
## Methods may be defined for arguments: con, format, text
## Use showMethods(import) for currently available ones.getGeneric("export")## standardGeneric for "export" defined from package "BiocIO"
##
## function (object, con, format, ...)
## standardGeneric("export")
## <bytecode: 0x55d63d456f78>
## <environment: 0x55d63d446878>
## Methods may be defined for arguments: object, con, format
## Use showMethods(export) for currently available ones.BiocFile is a base class for high-level file abstractions, where subclasses
are associated with a particular file format/type. It wraps a low-level
representation of a file, currently either a path/URL or connection.
CompressedFile is a base class that extends the BiocFile class that offers
high-level file abstractions for compressed file formats. As with the BiocFile
class, it takes either a path/URL of connection as an argument. This package
also includes other File classes that extend CompressedFile including:
BZ2File, XZFile, GZFile, and BGZFile which extends the GZfile class
In previous releases, rtracklayer package’s RTLFile, RTLList, and
CompressedFile classes threw errors when a class that extended them was
initialized. The error could have been seen with the LoomFile class from
LoomExperiment.
file <- tempfile(fileext = ".loom")
LoomFile(file)
### LoomFile object
### resource: file.loom
### Warning messages:
### 1: This class is extending the deprecated RTLFile class from
### rtracklayer. Use BiocFile from BiocIO in place of RTLFile.
### 2: Use BiocIO::resource()The first warning indicated that the RTLFile class from rtracklayer was
deprecated for future releases. The second warning indicated that the
resource method from rtracklayer was moved to BiocIO.
To resolve this issue, developers should simply replace the contains="RTLFile"
argument in setClass with contains="BiocFile".
## Old
setClass('LoomFile', contains='RTLFile')
## New
setClass('LoomFile', contains='BiocFile')The primary purpose of this package is to provide high-level classes and
generics to facilitate file IO within the Bioconductor package suite. The
remainder of this vignette will detail how to create File classes that extend
the BiocFile class and create methods for these classes. This section will
also detail using the filter and select methods from the tidyverse dplyr package
to facilitate lazy operations on files.
The CSVFile class defined in this package will be used as an example. The
purpose of the CSVFile class is to represent CSVFile so that IO operations
can be performed on the file. The following code defines the CSVFile class
that extends the BiocFile class using the contains argument. The CSVFile
function is used as a constructor function requiring only the argument
resource (either a character or a connection).
.CSVFile <- setClass("CSVFile", contains = "BiocFile")
CSVFile <- function(resource) .CSVFile(resource = resource)Next, the import and export functions are defined. These functions are meant to
import the data into R in a usable format (a data.frame or another
user-friendly R class), then export that R object into a file. For the CSVFile
example, the base read.csv() and write.csv() functions are used as the body
for our methods.
setMethod("import", "CSVFile", function(con, format, text, ...) {
read.csv(resource(con), ...)
})
setMethod("export", c("data.frame", "CSVFile"),
function(object, con, format, ...) {
write.csv(object, resource(con), ...)
}
)And finally a demonstration of the CSVFile class and import/export methods in
action.
temp <- tempfile(fileext = ".csv")
csv <- CSVFile(temp)
export(mtcars, csv)
df <- import(csv)## R version 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] BiocIO_1.14.0 BiocStyle_2.32.0
##
## loaded via a namespace (and not attached):
## [1] digest_0.6.35 R6_2.5.1 bookdown_0.39
## [4] fastmap_1.1.1 xfun_0.43 cachem_1.0.8
## [7] knitr_1.46 BiocGenerics_0.50.0 htmltools_0.5.8.1
## [10] rmarkdown_2.26 stats4_4.4.0 lifecycle_1.0.4
## [13] cli_3.6.2 sass_0.4.9 jquerylib_0.1.4
## [16] compiler_4.4.0 tools_4.4.0 evaluate_0.23
## [19] bslib_0.7.0 yaml_2.3.8 BiocManager_1.30.22
## [22] S4Vectors_0.42.0 jsonlite_1.8.8 rlang_1.1.3