clean. For cleaning flow cytometry data.

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Description

This function uses compositional data analysis to identify errant collection events.

Usage

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clean(fF, vectMarkers, filePrefixWithDir, ext, binSize=0.01,
  nCellCutoff=500, announce=TRUE, cutoff="median", diagnostic=FALSE, fcMax=1.3)

Arguments

fF

flowFrame object containing experimental data to be cleaned.

vectMarkers

A vector of indices representing flow parameters to be examined. These are considered as columns in the data matrix in which cells are rows and parameters are columns. Generally this vector excludes indices for various 'scatter' parameters (e.g. 'FSC-A')

filePrefixWithDir

A string containing at least the desired name for the output flow file generated. Can include directory structure and folder ('/' or '\') characters.

ext

The file extension for the output flow file.

binSize

A number in [0,1]; represents the fraction of duration of collection per bin.

nCellCutoff

An integer; represents the minimum number of cells a population must have to be included in analysis.

cutoff

Method for determining threshold for parameter. Can be "median" (default) or in [0, 1], which is interpreted as a perecntile. Integers > 1 will be interpreted as the fluorescence value to be used for a threshold.

announce

Print completion messages.

fcMax

Maximum allowable increase relative to presumed 'good' data.

announce

If TRUE, will print message to screen if errors detected.

diagnostic

If TRUE, will make PNG of populations in time bins, and save with same prefix as specified in filePrefixWithDir.

returnVector

If desired, only return vector indicating if a given cell is 'good' or 'bad'.

nstable

The number of stable populations required to be observed during the duration of an experiment. Default is 5.

Author(s)

Kipper Fletez-Brant

References

Fletez-Brant C, Spidlen J, Brinkman R, Roederer M and Chattopadhyay P. flowClean: Automated identification and removal of fluorescence anomalies in flow cytometry data. Cytometry Part A, 2016.

See Also

The package vignette.

Examples

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data(synPerturbed)
synPerturbed.c <- clean(synPerturbed, vectMarkers=c(5:17),
  filePrefixWithDir="sampleName", ext="fcs")

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