# BiocBaseUtils
The `BiocBaseUtils` package provides a suite of helper functions
designed to help developers. Currently, it covers three topics often
encountered during the development process.
1. Assertions - Type checks for logical, character, and numeric inputs
2. Slot replacement - Replacing the value of object slots
3. `show` method - Limiting the output of internal components of a
class
# Installation
Install the package directly from Bioconductor:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BiocBaseUtils")
```
# Load Package
``` r
library(BiocBaseUtils)
```
# Assertions
We provide a number of functions that helps the developer establish the
type of class of a particular object. These include `integer`,
`numeric`, `character`, and `logical`; types often used in R /
Bioconductor.
## Logical
``` r
isTRUEorFALSE(TRUE)
#> [1] TRUE
isTRUEorFALSE(FALSE)
#> [1] TRUE
isTRUEorFALSE(NA, na.ok = TRUE)
#> [1] TRUE
```
## Character
``` r
isScalarCharacter(LETTERS)
#> [1] FALSE
isScalarCharacter("L")
#> [1] TRUE
isCharacter(LETTERS)
#> [1] TRUE
isCharacter(NA_character_, na.ok = TRUE)
#> [1] TRUE
isZeroOneCharacter("")
#> [1] FALSE
isZeroOneCharacter("", zchar = TRUE)
#> [1] TRUE
```
## Numeric
``` r
isScalarInteger(1L)
#> [1] TRUE
isScalarInteger(1)
#> [1] FALSE
isScalarNumber(1)
#> [1] TRUE
isScalarNumber(1:2)
#> [1] FALSE
```
# Slot replacement
This function is often used in packages that establish formal S4
classes. When updating the value of a slot, one often uses the
`setSlots` function.
``` r
setClass("A", representation = representation(slot1 = "numeric"))
aclass <- new("A", slot1 = 1:10)
aclass
#> An object of class "A"
#> Slot "slot1":
#> [1] 1 2 3 4 5 6 7 8 9 10
```
Now we use the `setSlots` function to update the values in the object.
``` r
aclass <- setSlots(aclass, slot1 = 11:20)
aclass
#> An object of class "A"
#> Slot "slot1":
#> [1] 11 12 13 14 15 16 17 18 19 20
```
Note that `setSlots` provides the same functionality as
`BiocGenerics:::replaceSlots` but is more consistent with Bioconductor
the setter and getter language.
# `show` method
The `selectSome` function allows the developer to display a limited
amount of information from a developed class. Note that the use of the
`@` here is due to the minimal implementation in the examples provided.
The developer should always provide an interface to access the internal
components of the class via an ‘accessor’ function.
``` r
setMethod("show", signature = "A", function(object) {
s1info <- getElement(object, "slot1")
cat("A sequence:", selectSome(s1info))
})
aclass
#> A sequence: 11 12 ... 19 20
```
# Contributing
`BiocBaseUtils` is a work in progress and we welcome contributions.
There are quite a few often-used utility functions that are yet to be
included in the package. We would like to keep the dependencies in this
package minimal; therefore, contributions should mostly use base R.
# Session Info
``` r
sessionInfo()
#> R version 4.2.1 (2022-06-23)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.4 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
#>
#> locale:
#> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
#> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
#> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] stats graphics grDevices datasets utils methods base
#>
#> other attached packages:
#> [1] BiocBaseUtils_0.99.10
#>
#> loaded via a namespace (and not attached):
#> [1] compiler_4.2.1 magrittr_2.0.3 fastmap_1.1.0 htmltools_0.5.3
#> [5] tools_4.2.1 yaml_2.3.5 codetools_0.2-18 stringi_1.7.8
#> [9] rmarkdown_2.15 knitr_1.39 stringr_1.4.0 xfun_0.32
#> [13] digest_0.6.29 rlang_1.0.4 renv_0.15.5 evaluate_0.16
```
Please report minimally reproducible bugs at our [github issue
page](https://github.com/Bioconductor/BiocBaseUtils/issues).
