presAbsCall: Presence/absence call

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

Description

Adds a matrix to assayData (‘paData’) which indicates the presence/absence call for each gene in each sample using the background estimates and a stringency value. A gene is considered present in a sample if its count in that sample exceeds the corresponding background estimate times the stringency. The count values can be taken from either the positive control normalized data or the raw data (see the inputMatrix agrument). If the input doesn't contain background-corrected data, an error will be generated.

Usage

## S4 method for signature 'RccSet'
presAbsCall(rccSet, stringency = 2,
  inputMatrix = c("posCtrlData", "exprs"), quietly = FALSE)

Arguments

rccSet	An RccSet with background-corrected data.
stringency	Multiplier to use in establishing the presence/absence call as mentioned in the description.
inputMatrix	Name of the matrix in the RccSet's assayData on which to apply the presence/absence call (either "posCtrlData" or "exprs").
quietly	Logical. If TRUE, messages and warnings will not be shown.

Value

A copy of the input is returned with a new matrix named ‘paData’ added to the assayData that contains the presence/absence calls.

Examples

data(example_rccSet)
pcnorm_rccSet <- posCtrlNorm(example_rccSet)
bgEst <- getBackground(pcnorm_rccSet)
bgcorr_rccSet <- subtractBackground(pcnorm_rccSet, bgEst)
pa_rccset <- presAbsCall(bgcorr_rccSet)

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