包括现有包中S4对象作为新S4类中的槽

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，当我检查这个包时，我得到了以下警告：

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

这个类工作得很好(也就是，现在有错误了)，但我想修复代码中的所有警告。

包含DESeqDataSet对象(DESeq2，也是我们为插槽指定的名称)的包被导入到包DESCRIPTION文件中。我是否需要做一些其他的事情来使其内容在插槽中可用？例如，我使用setOldClass()使S3类可以在S4插槽中使用。

下面是一个抛出warning - https://travis-ci.org/caseywdunn/agalmar/builds/138564256的travis-ci构建示例

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

Answer 1

类定义需要导入，就像函数、泛型和方法一样。因此，在名称空间文件中

importClassesFrom("DESeq2", "DESeqDataSet")

我相信@importClassesFrom DESeq2 DESeqDataSet是roxygen2符号

Answer 2

您可以通过使用setClass函数的"contains“参数来解决问题。Contains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")
)

希望这能有所帮助。