qc_metrics: Quality control on the cells

In huipan1973/ezscrnaseq: What the Package Does (One Line, Title Case)

Quality control on the cells

Description

Quality control on the cells i.e. filter cells by library sizes, number of expressed genes and mitochondrial gene proportion, visualize the QC metrics by histograms.

Usage

qc_metrics(
  sce,
  sym_col = "symbol",
  by_nmads = TRUE,
  thresholds = c(3, 3, 3),
  ncores = 1,
  prefix = NULL,
  plot = TRUE,
  write = TRUE,
  verbose = TRUE
)

Arguments

sce	A SingleCellExperiment object containing expression values, usually counts.
sym_col	The column name for the gene symbols in rowData(sce).
by_nmads	TRUE/FASLE for using number of median absolute deviation as thresholds.
thresholds	Numbers of median absolute deviation if by_nmads is TRUE, otherwise the actual counts or percentages.
ncores	Number of cores.
prefix	Prefix for file name for the QC metrics histograms.
plot	TRUE/FASLE for whether plot the QC metrics histograms.
write	TRUE/FASLE for whether write the table of filtered cells.
verbose	TRUE/FASLE for specifying whether diagnostics should be printed to screen.

Value

A SingleCellExperiment object.

huipan1973/ezscrnaseq documentation built on July 12, 2022, 9:36 p.m.