Table of cells before / after QC

Source: R/preprocessing_filtering_reduction.R

Table of cells before / after QC

num_cell_after_QC_filt_scExp(scExp, annot, datamatrix)

Arguments

scExp

A SingleCellExperiment object.
annot

A raw annotation data.frame of cells before filtering.
datamatrix

A matrix of cells per regions before filtering.

Value

A formatted kable in HTML.

Examples

scExp = create_scExp(create_scDataset_raw()$mat,create_scDataset_raw()$annot)

#> ChromSCape::create_scExp - the matrix has 300 cells and 600 features.
scExp_filtered = filter_scExp(scExp)

#> ChromSCape::filter_scExp - 285 cells pass the  threshold of 1600 minimum reads and are lower than the 95th centile of library size ~= 14219 reads.
#> ChromSCape::filter_scExp - 600 features pass the threshold of 10 count per feature.
if (FALSE)  num_cell_after_QC_filt_scExp(
scExp_filtered,SingleCellExperiment::colData(scExp))