包括從現有的包作爲一個新的S4類別的插槽

Question

我寫信叫Expression一個S4級，並希望包括S4對象，DESeq2 = "DESeqDataSet"作爲插槽中的S4對象：

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" 
)) 

當我檢查包裝，不過，我得到以下警告：

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

類工作正常（即現在有錯誤），但我想修復我們的代碼的所有警告。

包含DESeqDataSet對象（DESeq2，也是我們給出的插槽名稱）的包將導入包DESCRIPTION文件中。我是否需要做其他事情才能使其內容在插槽中可用？例如，我使用setOldClass()使S3類可用於S4插槽。

這裏是一個特拉維斯-CI構建拋出警告的一個例子 - https://travis-ci.org/caseywdunn/agalmar/builds/138564256

那是給這個問題是在https://github.com/caseywdunn/agalmar/blob/a7c4013fcb5c924cfd6e1aa8e99f182ceec6fe20/R/utility_functions.R

Answer 1

類定義需要進口，就像函數的完整代碼，泛型和方法。所以在空間文件說

importClassesFrom("DESeq2", "DESeqDataSet") 

我相信roxygen2符號是@importClassesFrom DESeq2 DESeqDataSet

Answer 2

您可以通過使用「包含」 setClass函數的參數解決您的問題。包含可以定義任何類型或對象。

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") 
) 

希望這會有所幫助。