normQA {flowStats} | R Documentation

## 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

[Package flowStats version 4.2.0 Index]