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decontX包运行问题 #6

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octtt19 opened this issue Jan 18, 2024 · 1 comment

octtt19 commented Jan 18, 2024

您好，看了您单细胞分析流程，其中提到seurat是v5版本，所以想请问一下以下这部分是怎么运行的呀？

> ## 环境 RNA 校正
> ```R
> decontX_results <- decontX::decontX(sce@assays$RNA@counts) 
> sce$Contamination = decontX_results$contamination
> [email protected]

v5版本没有这个结构了‘sce@assays$RNA@counts‘，运行时会报错提示。

Error in h(simpleError(msg, call)) : 
  在为'decontX'函数选择方法时评估'x'参数出了错: "counts"槽名不存在于"Assay5"类别对象中

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Owner

limour-blog commented Jan 20, 2024

您好，当时 v5 刚出不久，因此只是顺便记录一下 v5 的安装过程，options(Seurat.object.assay.version = 'v5')并未实际使用，后续流程还是v4

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