cellQC: Quality control

Description Usage Arguments Details Value Examples

Description

Checks quality of all plates and then wells.

Usage

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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

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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"])

Bioconductor-mirror/OperaMate documentation built on May 31, 2017, 9:38 p.m.