Questions tagged [r-s4]
One of the methods of object oriented programming in the R language.
661
questions
4
votes
1
answer
100
views
Is there a way to prevent modification of an S4 object in R?
I want to create an S4 class that is a subclass of another S4 class, with additional constraints (like the object should be sorted). Given that modifications of the object could result in violations ...
- 183
1
vote
1
answer
26
views
How do I override auto formats in TERN functions like count_patients_with_flags?
TERN (Rtables) Package Formatting Functions
Anyone here familiar with overriding auto formats in TERN functions like count_patients_with_flags?
lyt_adae <- basic_table(show_colcounts = TRUE) %>%
...
- 11
1
vote
1
answer
84
views
Overriding the subset method in R for a specific class interferes with other objects
I am working with R and I have created a new subset method for objects of class new_object. Here is my function:
setGeneric('subset', function(x, i) standardGeneric('subset'))
setMethod('subset', '...
- 443
0
votes
0
answers
54
views
rewriting R6 to S4 class in R
I have this function here
person1$check_infection(person2)
person1 and person2 are R6 class objects, I have already rewritten the check_infection method in S4, how do I write the above function in S4?...
- 57
1
vote
0
answers
63
views
How to document a method in R using Roxygen2 when the class and generic live in another package?
How does one document a method for a class defined in another package?
For example, I've written a method for the QDNAseqSignals class defined in the QDNAseq. I want to document this method using ...
- 11
0
votes
1
answer
51
views
add personal funtion in setMethod in R
I have and new S4 object with 4 Slots, one of them is a data.frame (g_table), so I want to add a parameters to setMethod to subset the data:
this is my actual code:
setGeneric('g_table', function(x) ...
- 723
0
votes
0
answers
36
views
(R) Finding list elements by name and combine list elements into c()
I have an S4 object named "S4" that contains the id and a list (or it can be changed into a data frame) named "color" that has the color information annotated to each id in R.
# S4 ...
- 1
0
votes
1
answer
36
views
Using the `validate` package inside an Rmarkdown document
I wish to include same validations inside my Rmarkdown report. Here is a minimal example:
---
title: "My Report"
output:
html_document:
mode: selfcontained
theme: null
---
```{r, ...
- 18.2k
0
votes
0
answers
409
views
Subcluster all the clusters of a Seurat object
I have a Seurat object made from integrating 4 different objects, the results is a Seurat object with 70 clusters (0 to 69) I wanted to subset each single cluster and recluster it to achieve higher ...
- 55
0
votes
0
answers
119
views
How can I convert a RS4 object to python data frame?
I am trying to perform DGE analysis with Deseq2 in python using the rpy2 package. I have currently managed to reach the step where I have my results in the RS4 object format. Ideally now I would like ...
- 11
0
votes
0
answers
37
views
S4 method for ensuring dplyr distinct selects rows containing distinct S4 objects
I am implementing an S4 class called Taxa. Objects of class Taxa form a column in a tbl_df. For example:
my_tbl <- tibble::tibble(taxa = list(Taxa(Taxon(family = "test")), Taxa(Taxon(...
- 727
0
votes
0
answers
67
views
Issue with `mclapply` in R package S4 implementation when passing strings
I am developing an R package that utilizes S4 classes and methods. In one of the methods, I am using mclapply from the parallel package to process data in parallel. This method has an if-else nest ...
- 383
0
votes
1
answer
43
views
R Error message 'argument fdef is missing with no default`
The following code fails with the error message shown above.
#' Generic setter for XiFit class
#'
#' @param knots Knots object to which weights are applied
#' @param weights Given weights
#'
#' @...
- 457
1
vote
2
answers
73
views
Generating similar methods via loop in R package
I tried to write a for loop to create getters and setters for slots of an S4 class.
A similar reprex with a smaller class and only methods for the getters is:
library(methods)
library(testthat)
...
- 11
5
votes
1
answer
73
views
Is there a way to use own package's data (internal or external) as a default S4 class slot?
Is there a way to use my own package's data (internal or external) as a default S4 class slot?
If I create some package data:
my_pkg_data <- sample(100)
usethis::use_data(my_pkg_data, internal=...
