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EDePasquale / DoubletDecon

A tool for removing doublets from single-cell RNA-seq data
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Improved_Seurat_Pre_Process could not find function #29

Open rzhao0624 opened 4 years ago

rzhao0624 commented 4 years ago

Hello all,

I'm very new to coding and Seurat and everything here so my apologies in advance if this question doesn't have all the necessary coding information that one would need to answer. If you need further information I would be happy to provide.

I was trying to check doublelets in my seurat object using this packaged called DoubletDecon https://github.com/EDePasquale/DoubletDecon (here's the link)

First I did

Improved_Seurat_Pre_Process(object, num_genes=50, write_files=FALSE)

And then I got this error Error in Improved_Seurat_Pre_Process(ncc.madelaine.nodoub, num_genes = 50, : could not find function "Improved_Seurat_Pre_Process"

On the DoubletDecon package page, it says this funcion could be found in Seurat package. I do have Seurat package installed and running on RStudio so I don't know why it couldn't find this function. I'm using Seurat 3.1.1 and I also tried to install an older version of Seurat 3.0.0 but it still gave the same error message.

Could anyone please help me? Thank you so much in advance!

EDePasquale commented 4 years ago

Hi,

The Improved_Seurat_Pre_Process() is a function within DoubletDecon, not Seurat. If you could let me know where to find the confusing description I can update the wording.

Is it possible that you haven't loaded the DoubletDecon package with "library(DoubletDecon)" prior to running Improved_Seurat_Pre_Process()?

Best, Erica