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bicciatolab / popsicleR

popsicleR, a flexible R package aimed at providing most of the necessary quality controls and preliminary information for complete and detailed analysis of single cell RNA-seq data.
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Dissociation genes counted multiple times #2

Closed rdistefano closed 1 year ago

rdistefano commented 1 year ago

Digging down the QC metrics calculated by PopsicleR (compared Scanpy vs. PopsincleR), I found a potential error in the _percentdisso calculation. A few genes are counted multiple times. I would suggest going from:

dissociation_genes <- paste(dissociation_genes, collapse='|')

to

dissociation_genes <- paste('^', paste(dissociation_genes, collapse='$|^'), '$', sep = '')

Please, check this out.

bicciatolab commented 1 year ago

Dear Rosario, thank you for reporting this issue and for your kind suggestion.

We tested popsicleR on some different datasets and found that in some cases few genes could be counted multiple times as you noted.

We have already implemented your solution in our code and updated the package.

Thank you for your support.