normQA: Normalization quality assessment
In flowStats: Statistical methods for the analysis of flow cytometry data

Description Usage Arguments Details Value Author(s)

Create QA plots for a flow cytometry normalization process.

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

`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.

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

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

Florian Hahne

flowStats documentation built on Nov. 8, 2020, 6:49 p.m.