qaProcess.2DStatsPlot: Creates a QA process for 2D summary statistic comparisons...

In flowQ: Quality control for flow cytometry

Description

This function takes a list of flowSet as input and creates all necessary output for a '2DStatsPlot' type QA process. Objects created by this function can be laid out as HTML using writeQAReport.

Usage

 
 qaProcess.2DStatsPlot(flowList,dyes=c("FSC-A","SSC-A"),
			  outdir="QAReport",thresh=0.25,func=mean,
			  sum.dimensions=NULL,det.dimensions= NULL,pdf=TRUE,
			  name="2DStats",...)

Arguments

flowList	A list of flowSet
dyes	Flow parameters to be compared across multiple 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.
thresh	A numeric value between 0 and 1 which is used as a threshold by the outlier detection algorithm
func	Summary statistic function to be applied to each parameter in a flowFrame (mean,median etc)
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, default is NULL where the dimensions are automatically selected.
pdf	boolen value determinining if pdf files or jpeg images will be produced by the QA process
name	The name of the process used for the headings in the HTML output.
...	Further arguments.

Details

QA processes of type '2DStatsPlot' detects differences in the value of a summary statistic such as the mean, median etc across multiple samples.

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.marginevents, qaProcess.DensityPlot, qaProcess.ECDFPlot

Examples

data(qData)
dest <- tempdir()
par<-c("FSC-A","SSC-A","CD4","CD8")
resMean <- qaProcess.2DStatsPlot(qData,dyes=par,
                outdir=dest, func=mean, thresh=0.28,pdf=TRUE) 
resMean

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