qaProcess.timeline: Create QA process of type 'timeline'

In flowQ: Quality control for flow cytometry

Description

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

Usage

qaProcess.timeline(set, channels=NULL, outdir, cutoff=1,
  name="time line", sum.dimensions=NULL, det.dimensions=c(3,2),
  pdf=TRUE, ...)

Arguments

set	A flowSet
channels	A character vector of channel names for which the qaReport is to be produced. Will use all available channels except for the time channel if NULL.
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 for all of them.
cutoff	The threshold at which the QA criterion is considered to be failed. An absolute value in the timeline deviation score as computed by the timeLinePlot function.
name	The name of the process used for the headings in the HTML output.
sum.dimensions, det.dimensions	The dimensions of the pdf device in inches used for the summary and the detailed plots.
pdf	Logical indicating whether to create vectorized versions of images for this quality process. This should be set to FALSE if disk space is critical, since the pdf versions of the image consume much more space on the hard drive compared to the bitmap version.
...	Further arguments.

Details

QA processes of type 'timeline' detect unusal patterns in the acquisition of fluorescense and light scatter measurements over time. These are detected dynamically by identifying trends in the signal intensity over time or local changes in the measurement intensities. The underlying hypothesis is that measurement values are acquired randomly, hence there shouldn't be any correlation to time.

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

Value

An object of class qaProcess.

Author(s)

Florian Hahne

See Also

writeQAReport, qaReport, qaProcess, qaProcess.marginevents qaProcess.timeflow, qaProcess.cellnumber

Examples

## Not run: 
data(GvHD)
GvHD <- transform(GvHD, "FL1-H"=asinh(`FL1-H`), "FL2-H"=asinh(`FL2-H`))
dest <- tempdir()
qp <- qaProcess.timeline(GvHD, channel="FL1-H", outdir=dest, cutoff=1)
qp

## End(Not run)

flowQ documentation built on Nov. 1, 2018, 3:38 a.m.