cellQC: Quality control

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"), ...)
"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

Value

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

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).

Examples

Run this code

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"])