posSumVsAllSumPlot: posSumVsAllSumPlot

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

Description

Plot the ratio of sums of positive control counts to all counts for all samples in an RccSet object.

Usage

## S4 method for signature 'RccSet'
posSumVsAllSumPlot(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). (If the median ratio is less than 1, three times this value will be used.)

Details

The ratio for each sample in the RccSet is plotted and and outliers (as determined by 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.