qaProcess.marginevents {flowQ}R Documentation

Create QA process of type 'marginevents'

Description

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

Usage

qaProcess.marginevents(set, channels = NULL, grouping=NULL, outdir,
cFactor = 1, ...)

Arguments

set A flowSet
channels A character vector of channel names for which margin events are to be recorded
grouping A character vector defining one of the variables in the phenoData of set used as a grouping variable. If this argument is uses, comparisons will be made within groups rather than across all samples.
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.
cFactor The threshold at which the QA process is considered to have failed. This is the fold change of margin event percentages compared to the median percentage of events for the respective channel.
... Further arguments.

Details

QA processes of type 'marginevents' record the number of events that fall on the margins of the measurement range for each channel. Unproportionally high numbers of such events can indicate problems with the instrument settings.

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

Value

An object of class qaProcess.

Note

This function is still experimental

Author(s)

Florian Hahne

See Also

writeQAReport, qaReport, qaProcess, qaProcess.timeline, qaProcess.timeflow, qaProcess.cellnumber

Examples

## Not run: 
data(GvHD)
dest <- tempdir()
qp <- qaProcess.marginevents(GvHD, channels=c("FL1-H", "FL2-H"),
  outdir=dest)
qp
## End(Not run)

 

[Package flowQ version 1.2.0 Index]