将现有包中的S4对象包括为新S4类中的插槽

问题描述

我正在编写一个名为 Expression 的S4类，并希望包含一个S4对象， DESeq2 = DESeqDataSet 作为广告位：

I am writing an S4 class called Expression and would like to include an S4 object, DESeq2 = "DESeqDataSet" as a slot:

setClass(
Class = "Expression",
representation = representation (
    species = "character", 
    edgeR = "DGEList",
    DESeq2 = "DESeqDataSet",
    lengths = "matrix",
    individuals = "vector",
    treatments = "vector",
    id = "vector",
    samples = "vector",
    sample_prep = "vector",
    genome_type = "vector",
    molecule_type = "vector",
    blast_hit =  "vector",
    rRNA = "vector",
    protein = "vector"
))

但是，当我检查包裹时，会收到以下警告：

When I check the package, though, I get the following Warning:

Found the following significant warnings:
  Warning: undefined slot classes in definition of "Expression": DESeq2(class "DESeqDataSet")

课堂作业很好（即现在有错误），但是我想修复代码中的所有警告。

The class works fine (ie, there are now errors), but I would like to fix all warnings in our code.

带有 DESeqDataSet 对象（ DESeq2 ，也是我们给插槽指定的名称）导入包 DESCRIPTION 文件。我是否需要做其他事情以使其内容可用于插槽？例如，我使用 setOldClass（）使S3类可用于S4插槽。

The package with the DESeqDataSet object (DESeq2, also the name we have given to the slot) is imported in the package DESCRIPTION file. Do I need to do something else to make its contents available for use in a slot? For example, I have used setOldClass() to make S3 classes available for use in S4 slots.

这里是引发警告的travis-ci构建示例-

Here is an example of a travis-ci build that throws the warning - https://travis-ci.org/caseywdunn/agalmar/builds/138564256

给出问题的完整代码位于 https://github.com/caseywdunn/agalmar/blob/a7c4013fcb5c924cfd6e1

The full code that is giving the problem is at https://github.com/caseywdunn/agalmar/blob/a7c4013fcb5c924cfd6e1aa8e99f182ceec6fe20/R/utility_functions.R

推荐答案

需要导入类定义，就像函数，泛型和方法一样。因此，在NAMESPACE文件中说

Class definitions need to be imported, just like functions, generics, and methods. So in the NAMESPACE file say

importClassesFrom("DESeq2", "DESeqDataSet")

我相信roxygen2的表示法是 @importClassesFrom DESeq2 DESeqDataSet

I believe the roxygen2 notation is @importClassesFrom DESeq2 DESeqDataSet

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