5.1 QC report

To help assess the data quality and determine the cutoffs for data filtration, scMINER provides a function, drawSparseEsetQC(), to generate a html-format quality control report:

## To generate the 
drawSparseEsetQC(input_eset = pbmc14k_raw.eset, output_html_file = "/your-path/PBMC14k/PLOT/pbmc14k_rawCount.html", overwrite = TRUE)

## scMINER supports group-specific QC highlights
drawSparseEsetQC(input_eset = pbmc14k_raw.eset, output_html_file = "/your-path/PBMC14k/PLOT/pbmc14k_rawCount.html", overwrite = FALSE, group_by = "true_label")

The quality control report consists of 4 parts:

• Key Statistics: it highlights 5 key statistics of given eset object, including number of cells, number of genes, mean of genes per cell, mean of UMIs per cell and mean of cells per gene.
• Detailed statistics of key metrics: it summarizes and visualizes the detailed statistics of 5 key metrics that scMINER uses for filtration: nUMI, nFeature, pctMito, pctSpikeIn, nCell.
• Detailed statistics per cell and gene: it lists the detailed statistics of each gene and cell.
• Filtration cutoffs by scMINER: it provides the cutoffs estimated automatically by scMINER based on Median ± 3 * MAD (maximum absolute deviance), and the pseudo-filtration statistics on both genes and cells with these cutoffs.