flowStats (version 3.30.0)

normQA: Normalization quality assessment

Description

Create QA plots for a flow cytometry normalization process.

Usage

normQA(data, morph = c("^fsc", "^ssc"), channels, odat = NULL, ask = names(dev.cur()) != "pdf", grouping = NULL, tag.outliers = FALSE, peaksOnly = TRUE)

Arguments

data

a normalized flowSet.

morph

A character vector of channel names to use for the backgating into the morphological channels.

channels

The channels for which to create plots. Defaults to all normalized channels.

odat

The original data set, always needed if there are no warping functions available.

ask

Ask before creating a new plot.

grouping

A grouping variable in data's phenoData slot.

tag.outliers

Logical. Add sample name to outliers in the plots.

peaksOnly

Logical. Only use data when a peak was detected in a particular sample. If set to FALSE, a average peak location is estimated.

Value

This function is called for its side effect of generating plots.

Details

This function assumes that the necessary information has been added as attributes to data during the normalization procedure. Depending on the available information, a set of QA plots is generated. Available plots are:

Amount of peak adjustment Warping functions

Landmark classification confidence Backgating of peak events in morphological channels