setSegmentQCFlags {GeomxTools} | R Documentation |
Add segment QC flags to protocol data
setSegmentQCFlags(object, qcCutoffs = DEFAULTS)
object |
name of the object class to perform QC on
|
qcCutoffs |
list of cutoffs and thresholds to use for QC |
NanoStringGeoMxSet
object with QCFlags
data frame
appended to protocolData
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))