Some mistakes in RunCellQC function

[YongjieWangSarcoma]

Dear Dr. Hao Zhang,

I appreciate that you created this fantastic package. I like using it to analyze single-cell RNAseq data. However, the RunCellQC function could have a small mistake.

As you can see in the scripts and output below, after running RunCellQC, all cells' percent_mito, percent_ribo, and ribo_mito_ratio are the same value. This is not possible.

library(SCP)
library(tidyverse)

data("pancreas_sub")

[email protected]$orig.ident%>%unique()%>%length()
pancreas_sub <- RunCellQC(srt = pancreas_sub)

unique(pancreas_sub$nCount_RNA)%>%length()
unique(pancreas_sub$nFeature_RNA)%>%length()
unique(pancreas_sub$percent.mito)%>%length()
unique(pancreas_sub$percent.ribo)%>%length()
unique(pancreas_sub$ribo.mito.ratio)%>%length()

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[1] 1

Total cells: 1000
Cells which are filtered out: 46
... 32 potential doublets
... 14 outlier cells
... 0 low-UMI cells
... 0 low-gene cells
... 0 high-mito cells
... 0 high-ribo cells
... 0 ribo_mito_ratio outlier cells
... 0 species-contaminated cells
Remained cells after filtering: 954
[1] 923
[1] 752
[1] 1
[1] 1
[1] 1

Best regards,
Yongjie Wang, MD/PhD