spillover_match-flowSet: Construct a 'flowSet' for use with 'spillover' by matching...

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

Construct a flowSet for use with spillover by matching channel names to compensation control filenames

Description

Spillover information for a particular experiment is often obtained by running several tubes of beads or cells stained with a single color that can then be used to determine a spillover matrix for use with compensate.

This method facilitates construction of a flowSet of compensation control flowFrames using a simple file linking filenames to channels. This resulting flowSet can then be used with spillover using the option prematched = TRUE.

Matching stain channels to compensation controls is done via a csv file (matchfile) with columns 'filename' and 'channel'. The 'channel' entries should exactly match the channel names in the FCS files. The 'filename' should be the FCS file name of each compensation control which should also be the corresponding sample name in the flowSet. There should also be one unstained control with the 'channel' entry of 'unstained'.

The method also allows for x to be missing if path is provided, pointing to a directory containing the control FCS files.

Usage

## S4 method for signature 'flowSet'
spillover_match(x, fsc = "FSC-A", ssc = "SSC-A",
                                    matchfile = NULL, path)

## S4 method for signature 'missing'
spillover_match(x, fsc = "FSC-A", ssc = "SSC-A", matchfile, path)

Arguments

x	A flowSet of compensation beads or cells
fsc	The name or index of the forward scatter parameter
ssc	The name or index of the side scatter parameter
matchfile	The name or path of the csv file holding the compensation control file to channel matching information.
path	The name or path of the directory containing the control FCS files to be matched to channels by matchfile.

Value

A flowSet with the sample names of its flowFrames corresponding to the channels specified by the matchfile.

Author(s)

B. Ellis, J. Wagner

See Also

compensate, spillover

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