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(NAcharacter, 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] LCCTYPE=C.UTF-8 LCNUMERIC=C LC_TIME=C.UTF-8

> [4] LCCOLLATE=C.UTF-8 LCMONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8

> [7] LCPAPER=C.UTF-8 LCNAME=C LC_ADDRESS=C

> [10] LCTELEPHONE=C LCMEASUREMENT=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] compiler4.2.1 magrittr2.0.3 fastmap1.1.0 htmltools0.5.3

> [5] tools4.2.1 yaml2.3.5 codetools0.2-18 stringi1.7.8

> [9] rmarkdown2.15 knitr1.39 stringr1.4.0 xfun0.32

> [13] digest0.6.29 rlang1.0.4 renv0.15.5 evaluate0.16

```

Please report minimally reproducible bugs at our github issue page.