qaProcess.ECDFPlot: Creates a QA process for comparisons of ECDF's across...

In flowQ: Quality control for flow cytometry

Description

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

Usage

 
 qaProcess.ECDFPlot(flowList, dyes=NULL,outdir="QAReport",
		    alpha=0.05, absolute.value=NULL,sum.dimensions=NULL,
		    det.dimensions=NULL, pdf=TRUE,  
		    name="ECDF",...)

Arguments

flowList	A list of flowSet
dyes	Flow parameters to be compared across multiple samples. If set to NULL, all parameters that are duplicated across the list of flowSet are identified and compared.
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.
alpha	Outlier mislabeling rate
absolute.value	If provided, the absolute.value is used for the outlier detection and the alpha argument is ignored. defualt is NULL
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 'ECDFPLot' detects differences in the empirical cumulative distribution of flow parameters across multiple samples.A summary measure based on the sum of the pairwise KL Distances of ECDF plots across multiple samples is used as a parameter to flag patient panels that are potential outliers.

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.DensityPlot qaProcess.marginevents, qaProcess.2DStatsPlot

Examples

data(qData)
dyes<- c("FSC-A","SSC-A")
dest <- tempdir()
resFSCECDF <- qaProcess.ECDFPlot(qData, dyes=dyes, outdir=dest,
                alpha=0.4, pdf=TRUE)
resFSCECDF

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