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

In flowQ: Quality control for flow cytometry

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,side ="both", grouping=NULL, 
    outdir, cFactor=2, absolute.value=NULL, name="margin events",
    sum.dimensions=NULL, det.dimensions=c(3,1), pdf=TRUE, ...)

Arguments

set	A flowSet.
channels	A character vector of channel names for which margin events are to be recorded. Will use all available channels except for the time channel if NULL.
side	Object of class "character". The margin on which to evaluate the filter. Either upper for the upper margin or lower for the lower margin or both for both margins.
grouping	A character vector defining one of the variables in the phenoData of set used as a grouping variable. If this argument is used and if absolute.value is NULL, outlier detection will be performed 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 for all of them.
cFactor	The outlier threshold at which the QA criterion is considered to have failed. This is essentially the factor of standard deviations away from the average number of cells per sample for the respective channel.
absolute.value	An absolute percentage of margin events below which the QA criterion is considered to be failed. If this argument is not NULL, cFactor is ignored.
name	The name of the process used for the headings in the HTML output.
sum.dimensions	The dimensions of summary plot generated in inches, default is NULL where the dimensions are automatically selected
det.dimensions	the dimensions of each sub image generated by the QA process in inches.
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. Setting the argument to FALSE will also speed up the process.
...	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 or with compensation. These are either determined dynamically as outliers from the typical distribution of margin event percentages for the whole set, or, if absolute.value is not NULL, by an absolute cutoff value. If there is a natural grouping among the samples, this can be specified using the grouping argument. In this case, the outlier detection will be performed within its respective group for a particular sample.

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.timeline, qaProcess.timeflow, qaProcess.cellnumber

Examples

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

## End(Not run)

 

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