s4

This is borrowed from shiny's function exprToFunction which is used in their reactive function. Actual question How can I delay the evaluation of an expression (e.g. specified via arg expr ) in order to "capture" its content when calling a S4 method (as opposed to a standard R function)? Example Note that x_1 does not exist yet, that's why we want to delay the evaluation of expr and just "capture" its content. Function captureExpression : captureExpression <- function( expr, caller_offset = 1, brackets = TRUE ) { out <- eval(substitute(substitute(expr)), parent.frame(caller_offset)) if

Actual questions Shouldn't the fact that R6 classes inherit from (informal S3) class R6 allow the definition of S4 methods for signature arguments of that very class? As this is - AFAICT - not the case, what would be a workaround that is in line with current S3/S4 standards or that could somewhat be regarded as "best practice" in such situations? Background and example Reference Classes Consider the following example where you would like to define methods that dispatch on the superclass that all instances of Reference Classes inherit from ( envRefClass ): TestRefClass <- setRefClass(

I'm trying to create a method for my class, which inherits from data.frame. I was originally hoping just to inherit the 'show' method from data.frame as well, but I'm also fine with writing my own. I defined my class and 'show' method as follows: setClass("SCvec", representation(auth = "character", dev = "character", sensor = "character", channel = "character", starttime = "character", endtime = "character"), contains="data.frame") setMethod("show", signature(x="SCvec"), function(x) print(x)) when I type show in the R console, it prints out: standardGeneric for "show" defined from package

Suppose I have an S4 class with two slots. I then create a method that sets one of the slots to something and returns the result. Will the other slot also be copied on assignment? For example, setClass('foo', representation(first.slot = 'numeric', second.slot = 'numeric')) setGeneric('setFirstSlot', function(object, value) {standardGeneric('setFirstSlot')}) setMethod('setFirstSlot', signature('foo', 'numeric'), function(object, value) { object@first.slot = value return(object) }) f <- new('foo') f@second.slot <- 2 f <- setFirstSlot(f, 1) On the last line, will the values of both the first and

I'm new to R. I'm trying to define a class similar to a tree node, that is , it has a left node and right node, which should be of the same class as the parent node. So I define the class as follows: setClass('Node', representation=(left='Node',right='Node', ...)) I want to set the default value of Node to be NULL by setting a prototype, but R says the following: invalid class "Node" object: invalid object for slot "left" in class "bicluster": got class "NULL", should be or extend class "Node" But if I don't speficy the default value to be NULL, then the default value will be a recursive Node

I have an object of S4 class like below: > gadem Object of class 'gadem' This object has the following slots: motifs,pwm,consensus,align,name,seq,chr,start,end,strand,seqID,pos,pval,fastaHeader > gadem[[1]] An object of class "motif" Slot "pwm": 1 2 3 4 5 6 7 8 9 10 11 A 0.3404 0 0.0000 0.6375 0.2723 0.3173 0 0.0002 0.3126 0 0.4969 C 0.4281 0 0.8708 0.1474 0.0767 0.1122 0 0.0000 0.0981 1 0.2558 G 0.1414 0 0.0000 0.0361 0.4153 0.5088 0 0.1134 0.0532 0 0.0000 T 0.0901 1 0.1292 0.1790 0.2357 0.0617 1 0.8864 0.5361 0 0.2473 Slot "consensus": [1] "mTCAnrTTwCm" Slot "alignList": [[1]] An object of

dbGetQuery is an S4 generic in RMongo . It is declared as dbGetQuery(rmongo.object, collection, query, skip=0, limit=1000) With a function like this in R, skip and limit are optional arguments. However, when I call it in this way dbGetQuery(mongo, 'changesPerTypeEpoch', '{}', limit=10000) I get an error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘dbGetQuery’ for signature ‘"RMongo", "character", "character", "missing", "numeric"’ Looking at the source code, I found there are two signatures defined for the generic: signature(rmongo.object=