cellQC: Quality control

In OperaMate: An R package of Data Importing, Processing and Analysis for Opera High Content Screening System

Description

Checks quality of all plates and then wells.

Usage

cellQC(object, qcType = NULL, qc.threshold = NULL,
  replace.badPlateData = TRUE, plot = TRUE,
  outpath = getOption("opm.outpath"), ...)

## S4 method for signature 'cellData'
cellQC(object, qcType = getOption("opm.QC.type"),
  qc.threshold = getOption("opm.QC.threshold"),
  replace.badPlateData = getOption("opm.replace.badPlateData"), plot = TRUE,
  outpath = getOption("opm.outpath"), ...)

Arguments

object	a cellData object
qcType	the type of quality control
qc.threshold	quality control thresholds
replace.badPlateData	if TRUE, replace the values of bad plate by their replicates
plot	if TRUE, plot figures
outpath	directory of output figures, default: getOption("opm.outpath")
...	arguments for the graphic device

Details

Requires three or more replicated samples.

qcType include c("plateCorrelation", "wellSd", "zFactor", "cellNumber"), An example of qc.threshold is c(correlation = 0.8, zfactor = 0.5, cellnumber = 50).

Value

a cellData object with intialized slot qc.data, plate.quality and plate.quality.data.

Examples

data(demoCell)
op <- options("device")
options("device" = "png")
oneCell <- cellQC(oneCell, qcType = c("plateCorrelation", "wellSd", "cellNumber"),
qc.threshold = c(correlation = 0.7), outpath = tempdir())
options(op)
str(oneCell["qc.data"])
str(oneCell["plate.quality"])

OperaMate documentation built on Nov. 17, 2017, 1:55 p.m.