Comprehensive reporting of QC metrics: computing per cell QC metrics usind addPerCellQC"

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

require(singleCellTK)
require(umap)
require(ggplot2)

sce.qc<- params$object

    plotsQCMetrics<- suppressWarnings(plotRunPerCellQCResults(sce.qc))
    i="QCMetrics"
    cat(paste0('# ', i, ' {.tabset .tabset-fade} \n\n'))
    cat(paste0('## Sum \n\n'))
    plotsQCMetrics$sum
    cat(paste0('## Total \n\n'))
    plotsQCMetrics$detected
    cat(paste0('## Subsets mito sum \n\n'))
    plotsQCMetrics$subsets_mito_sum
    cat(paste0('## Subsets mito detected \n\n'))
    plotsQCMetrics$subsets_mito_detected
    cat(paste0('## Subsets mito percent \n\n'))
    plotsQCMetrics$subsets_mito_percent
    cat(paste0('## Session info \n\n'))
    sce.qc@metadata$scater$addPerCellQC

description_runPerCellQC <- descriptionRunPerCellQC()

{.unlisted .unnumbered .toc-ignore}

r description_runPerCellQC

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.