iqrPlot: iqrPlot

In NanoStringQCPro: Quality metrics and data processing methods for NanoString mRNA gene expression data

Description

Plot the interquartile range (IQR) for a certain code class of probes in an RccSet object.

Usage

## S4 method for signature 'RccSet'
iqrPlot(rccSet, codeClass = c("Negative", "Positive",
  "Endogenous", "Housekeeping"), method = c("cutoffByMMAD", "cutoffByVar"),
  stringency = 4)

Arguments

rccSet	An RccSet object
codeClass	Character string specifying the code class (as annotated in the fData(rccSet)$CodeClass column) for which the IQR shall be determined.
method	Character string specifying the method for outlier detection: either "cutoffByMMAD" or "cutoffByVar".
stringency	Numeric value passed to the cutoff function specified by the method argument (see the 'd' argument of cutoffByMMAD and cutoffByVar).

Details

IQR of the specified code class for each sample in the RccSet are plotted and outliers (as determined by the function specified in the method argument) are marked in red (thresholds for outlier definition are plotted as red dashed lines).

Value

A plot

Author(s)

Dorothee Nickles

See Also

cutoffByMMAD, cutoffByVar

NanoStringQCPro documentation built on Nov. 8, 2020, 8:11 p.m.