Comprehensive reporting of QC metrics: predicting doublets with doubletFinder"

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

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

sce.qc<- params$object

    plotDoubletFinder<- suppressWarnings(plotDoubletFinderResults(inSCE = sce.qc, reducedDimName = "UMAP"))
    i="DoubletFinder"
    cat(paste0('# ', i, ' {.tabset} \n\n'))
    cat(paste0('## Scatter Score Resolution 1.5 \n\n'))
    plotDoubletFinder$Scatter_Score_Resolution_1.5

    cat(paste0('## Scatter Call Resolution 1.5 \n\n'))
    plotDoubletFinder$Scatter_Call_Resolution_1.5

    cat(paste0('## Density Resolution 1.5 \n\n'))
    plotDoubletFinder$Density_Resolution_1.5

    cat(paste0('## Violin Resolution 1.5 \n\n'))
    plotDoubletFinder$violin_Resolution_1.5

    cat(paste0('## Session info \n\n'))
    sce.qc@metadata$runDoubletFinder

description_DoubletFinder <- descriptionDoubletFinder()

{.unlisted .unnumbered .toc-ignore}

r description_DoubletFinder

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