calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics

Question

[otieno43]

Hello, I am trying to follow a tutorial from Sanger institute (from May 2019) on analysis of single cell RNA Seq data. They use calculateQCMetric function to calculate the quality metrics, but when I tried the same command, I am getting an error message that calculateQCMetric is a deprecated:

sce <- calculateQCMetrics(sce, feature_controls=list(Mito=which(location=="MT")))

Error:
Error: 'calculateQCMetrics' is defunct.
Use 'perCellQCMetrics' instead.
See help("Defunct")

I tried the perCellQCMetrics instead of calculateQCMetrics, I also ended up with an error.

sce <- perCellQCMetrics(sce, feature_controls=list(Mito=which(location=="MT")))

Error in .per_cell_qc_metrics(assay(x, assay.type), subsets = subsets,  : 
  unused argument (feature_controls = list(33653:33665))

Any help on how to resolve this error, please.

Erick

[Nitin Narwade]

Just out of curiosity why are you using the Sanger Institute's Single Cell Analysis tutorial from 2019, why not the recent one?

About this error, it is written perCellQCMetrics function does not have an option of feature_controls. Looking at their documentation I think you need the subsets option instead.

subsets : For the SummarizedExperiment and SingleCellExperiment methods, further arguments to pass to the ANY method. A named list containing one or more vectors (a character vector of feature names, a logical vector, or a numeric vector of indices), used to identify interesting feature subsets such as ERCC spike-in transcripts or mitochondrial genes.