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---
title: "BiocBaseUtils Quick Start"
author: "Bioconductor Core Team"
date: "`r format(Sys.time(), '%B %d, %Y')`"
output:
BiocStyle::html_document:
number_sections: yes
toc: true
vignette: >
%\VignetteIndexEntry{BiocBaseUtils Quick Start}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
# 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,eval=FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BiocBaseUtils")
```
# Load Package
```{r,include=TRUE,results="hide",message=FALSE,warning=FALSE}
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)
isTRUEorFALSE(FALSE)
isTRUEorFALSE(NA, na.ok = TRUE)
```
## Character
```{r}
isScalarCharacter(LETTERS)
isScalarCharacter("L")
isCharacter(LETTERS)
isCharacter(NA_character_, na.ok = TRUE)
isZeroOneCharacter("")
isZeroOneCharacter("", zchar = TRUE)
```
## Numeric
```{r}
isScalarInteger(1L)
isScalarInteger(1)
isScalarNumber(1)
isScalarNumber(1:2)
```
# 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
```
Now we use the `setSlots` function to update the values in the object.
```{r}
aclass <- setSlots(aclass, slot1 = 11:20)
aclass
```
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
```
# 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()
```
Please report minimally reproducible bugs at our [github issue page][].
[github issue page]: https://github.com/Bioconductor/BiocBaseUtils/issues
|
