setSeqQCFlags {GeomxTools} | R Documentation |
Add sequencing QC flags to NanoStringGeoMxSet object protocol data
setSeqQCFlags(object, qcCutoffs = DEFAULTS)
object |
name of the NanoStringGeoMxSet object to perform QC on |
qcCutoffs |
a list of qc cutoffs to use
|
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")) setSeqQCFlags(demoData, qcCutoffs=list(minSegmentReads=1000, percentAligned=80, percentSaturation=50))