qaProcess.BoundaryPlot {flowQ}R Documentation

Creates a QA process for comparison of the percentage of boundary events for the specified parameters across multiple samples

Description

This function takes a list of flowSet as input and creates all necessary output for a 'BoundaryPlot' type QA process. Objects created by this function can be laid out as HTML using writeQAReport.

Usage

 
 qaProcess.BoundaryPlot(flowList,dyes=NULL,
                          outdir="QAReport",cutoff=3,
                          det.dimensions=c(400,400),pdf=FALSE,...)

Arguments

flowList A list of flowSet
dyes Flow parameters to be compared across multiple samples. If set to NULL, all parameters that are duplicated across the list of flowSet are identified and compared.
outdir The directory to which the graphical output is to be saved. If multiple QA processes are to be combined, make sure to use the same directory every time.
cutoff A numeric value for the percentage of boundary events that is used by the process to identify samples that failed the QA process
det.dimensions the dimensions of each image generated by the QA process.
pdf boolen value determinining if pdf files or jpeg images will be produced by the QA process
... Further arguments.

Details

QA processes of type 'BoundaryPlot' helps identify samples that have a large number of boundary events that must be removed by further gating before detailed analysis of the data.

For more details on how to layout qaProcess objects to HTML, see writeQAReport and qaReport.

Value

An object of class qaProcess.

Author(s)

Nishant Gopalakrishnan

See Also

writeQAReport, qaReport, qaProcess,qaProcess.DensityPlot, qaProcess.ECDFPlot

Examples

data(qData)
dest <- tempdir()
resBoundary <- qaProcess.BoundaryPlot(qData, dyes=c("FSC-A","CD3"), 
                                      outdir=dest, cutoff=3, pdf=TRUE)
resBoundary

[Package flowQ version 1.4.0 Index]