RNAseq scater error in plotQC()
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@vladimir-krasikov-5097
Last seen 23 months ago

Dear creators/maintainers of the scater package

First of all, thanks for slim and intuitive package for the scRNAseq data

It is my first go with scRNAseq data and I try to follow scater vignettes

 

Looks like there might be a little bug in plotQC()

It happened that  my SingleCellExperiment object has only 'logcounts' data (no original 'counts)

when calling first:

sce <- calculateQCMetrics(sce, exprs_values = "logcounts")

and then

plotQC(sce, type = "highest-expression", exprs_values = "logcounts")

an error appears:

Error in .qc_hunter(object, "total_features_by_counts", mode = "column") : 
  failed to find 'total_features_by_counts' in column metadata

 

Looks like that despite  "total_features_by_logcounts" plotQC still requires  'total_features_by_counts'

Fix needed

Thanks

scater plotQC scRNAseq • 490 views
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Aaron Lun ★ 27k
@alun
Last seen 29 minutes ago
The city by the bay

Thanks for the bug report. This will be fixed in the latest version of scater. In the meantime, you can manually set the colour_cells_by argument to "total_features_by_logcounts" to avoid the error.

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