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compbiomed / singleCellTK

Interactively analyze single cell genomic data
https://camplab.net/sctk/
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Weird error with reportCellQC function #751

Open yingzhang121 opened 2 months ago

yingzhang121 commented 2 months ago

Hi, I got the following error message when I tried to run function "reportCellQC":

> reportCellQC(cellSCE)

processing file: CellQC.Rmd
  |..........                                        |  19%                                  

  |..................................                |  69%                                  
  |.......................................           |  78% [DecontX-plot]                   
Quitting from lines 1024-1060 [DecontX-plot] (CellQC.Rmd)
Error in `as.character()`:
! cannot coerce type 'closure' to vector of type 'character'
Backtrace:
 1. singleCellTK (local) metaChecking(DecontXMeta, sample)

So I copied the CellQC.Rmd from this github repository, and ran the knitting with assigning the correct "params" for inSCE object. The code finished without a problem, and you can see it here:

https://zhan2142.s3.msi.umn.edu/Parse_Lee_s47053_QC.html

I don't know why the markdown file worked fine, while the wrapper function "reportCellQC" failed.

My running environment is provided in the "sessionInfo" in the linked html file.