setBackgroundQCFlags: Add background QC flags to NanoStringGeoMxSet object protocol...

In Nanostring-Biostats/GeomxTools: NanoString GeoMx Tools

Add background QC flags to NanoStringGeoMxSet object protocol data

Description

Add background QC flags to NanoStringGeoMxSet object protocol data

Usage

setBackgroundQCFlags(object, qcCutoffs = DEFAULTS)

Arguments

object	name of the NanoStringGeoMxSet object to perform QC on
qcCutoffs	a list of qc cutoffs to use minNegativeCount, numeric to flag segments with less than this number of counts maxNTCCount, numeric to flag segments with more than this number of NTC counts

Value

NanoStringGeoMxSet object with QCFlags data frame appended to protocolData

Examples

datadir <- system.file("extdata", "DSP_NGS_Example_Data",
                       package="GeomxTools")
demoData <- readRDS(file.path(datadir, "/demoData.rds"))
setBackgroundQCFlags(demoData[,1:10], 
                 qcCutoffs=list(minNegativeCount=10, 
                                maxNTCCount=60))

Nanostring-Biostats/GeomxTools documentation built on Sept. 24, 2024, 4:51 p.m.