Question

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"作为插槽：

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，我收到以下警告：

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

该类工作正常（即，现在有错误），但我想在我们的代码中修复所有警告。

包DESeqDataSet对象（DESeq2，也是我们给插槽的名称）的包将导入包DESCRIPTION文件中。我是否需要做其他事情才能使其内容可用于插槽？例如，我使用setOldClass()使S3类可用于S4插槽。

以下是一个抛出警告的travis-ci构建示例 - https://travis-ci.org/caseywdunn/agalmar/builds/138564256

提供问题的完整代码位于https://github.com/caseywdunn/agalmar/blob/a7c4013fcb5c924cfd6e1aa8e99f182ceec6fe20/R/utility_functions.R

Answer 1

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

importClassesFrom("DESeq2", "DESeqDataSet")

I believe the roxygen2 notation is @importClassesFrom DESeq2 DESeqDataSet

Answer 2

您可以使用＆＃34; contains＆＃34;来解决您的问题。 setClass函数的参数。包含可以定义任何类型或对象。

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"
    ), 
    contains = c("DGEList", "DESeqDataSet")
)

希望这有帮助。

将现有包中的S4对象作为新S4类中的插槽包含在内

2 个答案: