normQA: Normalization quality assessment

In RGLab/flowStats: Statistical methods for the analysis of flow cytometry data

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.

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

Value

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

Author(s)

Florian Hahne

RGLab/flowStats documentation built on July 20, 2023, 1:33 a.m.