qaProcess.cellnumber {flowQ}R Documentation

Create QA process of type 'cellnumber'

Description

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

Usage


qaProcess.cellnumber(set, grouping=NULL, outdir, cFactor=0.5,
   name="cell number", sum.dimensions=c(7,7), ...)

Arguments

set A flowSet
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 be failed. The factor of standard deviations away from the average number of cells per sample
name The name of the process used for the headings in the HTML output
sum.dimensions The pdf dimensions used for the summary.
... Further arguments.

Details

QA processes of type 'cellnumber' detect aberations in the number of cells analyzed per frame.

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.timeline

Examples

## Not run: 
data(GvHD)
dest <- tempdir()
qp <- qaProcess.cellnumber(GvHD, outdir=dest, cFactor=1)
qp
## End(Not run)


[Package flowQ version 1.2.0 Index]