cytofQCreport: Generate a cytofQC report

In jillbo1000/cytofQC: Labels normalized cells for CyTOF data and assigns probabilities for each label

Generate a cytofQC report

Description

Generate a cytofQC report

Usage

cytofQCreport(x, outDir, sampName, runUMAP = TRUE, ...)

Arguments

x	A SingleCellExperiment object generated by labelQC.
outDir	The output directory (currently required).
sampName	Basename of the output HTML file (if not provided, same as outDir).
runUMAP	Logical value indicating whether or not to include a UMAP plot in the report. This plot can be beneficial for diagnostic purposes, but is time-consuming to generate.
...	Additions arguments that may be passed to the function.

Value

If successful, returns TRUE silently and generates the specified QC report.

Examples

data("raw_data", package = "CATALYST")
x <- readCytof(raw_data, beads = "Beads", viability = c("cisPt1", "cisPt2"))
x <- labelQC(x, n = 500)
tmp <- tempdir()
cytofQCreport(x, tmp, 'example')

jillbo1000/cytofQC documentation built on Aug. 23, 2023, 9:47 p.m.