setSegmentQCFlags {GeomxTools}

R Documentation

Add segment QC flags to protocol data

Description

Add segment QC flags to protocol data

Usage

setSegmentQCFlags(object, qcCutoffs = DEFAULTS)

Arguments

object	name of the object class to perform QC on NanoStringGeoMxSet, use the NanoStringGeoMxSet class
qcCutoffs	list of cutoffs and thresholds to use for QC

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"))
setSegmentQCFlags(demoData, 
                  qcCutoffs=list(minSegmentReads=1000, 
                                 percentAligned=80, 
                                 percentSaturation=50,
                                 minNegativeCount=10, 
                                 maxNTCCount=60,
                                 minNuclei=16000, 
                                 minArea=20))

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