allSumPlot: allSumPlot

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

Description

Plot the sum of all counts (endogenous and housekeeping genes only) for each sample in an RccSet object.

Usage

## S4 method for signature 'RccSet'
allSumPlot(rccSet, method = c("cutoffByMMAD",
  "cutoffByVar"), stringency = 4)

Arguments

rccSet	An RccSet object
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

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

Value

A plot

Author(s)

Dorothee Nickles

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