运行来自 rpy2 的 DESeq2

Question

我第一次尝试通过 rpy2 运行 DESeq2，但遇到了一些困难。

class py_DESeq2:
    
    def __init__(self, count_matrix):
        
        self.dds = None
        self.normalized_count_matrix = None
        self.vsd = None
        self.count_matrix = robjects.conversion.py2rpy(count_matrix)
        self.design_matrix = robjects.conversion.py2rpy(pd.DataFrame({'treatment':['ctrl' for i in range(count_matrix.shape[1])]}))
        self.design_formula = Formula('~ 1')
        
    def norm_counts(self, **kwargs):
        self.dds = deseq.DESeqDataSetFromMatrix(countData=self.count_matrix, colData=self.design_matrix, design=self.design_formula)
        self.vsd = deseq.varianceStabilizingTransformation(self.dds, blind=True)
        self.normed_count_matrix = deseq.assay(self.vsd)
        self.normed_count_matrix = to_dataframe(self.normed_count_matrix)
        self.normed_count_matrix = robjects.conversion.rpy2py(self.normed_count_matrix)

我在 self.normed_count_matrix = deseq.assay(self.vsd) 收到以下错误：

module 'DESeq2' has no attribute 'assay'

R 中的以下代码运行没问题：

library(DESeq2)
countData <- read.delim("0.333404867983521.R.data.in.txt")
colData <- read.delim("0.333404867983521.R.groups.in.txt")

dds <- DESeqDataSetFromMatrix(countData, colData,design=~Treatment,tidy=TRUE)
norm <- varianceStabilizingTransformation(dds,blind=TRUE)
norm_matrix <- assay(norm)
norm_df <- data.frame(Gene=rownames(norm_matrix), norm_matrix)
write.table(norm_df, "0.333404867983521.R.data.out.txt", row.names = FALSE,sep="\t")

规范对象是<class 'rpy2.robjects.methods.RS4'>。

这里一定有我遗漏的地方，不胜感激！

Answer 1

如果您打开 R 并输入：

library(DESeq2)
assay

你会看到 assay 函数实际上并不是来自 DESeq2，而是来自它的依赖项 SummarizedExperiment:

> assay
standardGeneric for "assay" defined from package "SummarizedExperiment"

function (x, i, withDimnames = TRUE, ...) 
standardGeneric("assay")
<bytecode: 0x5586a354db90>
<environment: 0x5586a3535e20>
Methods may be defined for arguments: x, i
Use  showMethods("assay")  for currently available ones.

您可以通过在 R:

中使用显式命名空间来确认 assay 不是 DESeq2 的一部分

> DESeq2::assay
Error: 'assay' is not an exported object from 'namespace:DESeq2'

并确认它确实是 SummarizedExperiment 的一部分：

> SummarizedExperiment::assay
standardGeneric for "assay" defined from package "SummarizedExperiment"

因此在 rpy2 中你可以这样使用它：

from rpy2.robjects.packages import importr

summarized_experiment = importr('SummarizedExperiment')
summarized_experiment.assay(self.vsd)

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