NanoStringGeoMxSet-class
                        Class to Contain NanoString Spatial Expression
                        Level Assays
aggregateCounts         Aggregate probe counts to target level for
                        feature data
as.Seurat               Convert GeoMxSet Object to SeuratObject
as.SpatialExperiment    Convert Object to SpatialExperiment
checkQCFlags            Check QC Flags in the GeoMxSet and removes the
                        probe or sample from the object
checkQCFlags,NanoStringGeoMxSet-method
                        checkQCFlags
compareToConfig         Compare given PKC probes to probes in config
                        file
computeNormalizationFactors
                        Generate normalization factors
countsShiftedByOne      Accessor to check if "exprs" 'assDataElement'
                        was shifted by one
hkNames                 Return the House Keeper positive controls for
                        protein
iggNames                Return the IgG negative controls for protein
logtBase                Get take the log of a numeric vector
mixedModelDE            Run a mixed model on GeoMxSet
ngeoMean                Get the geometric mean of a vector
ngeoSD                  Get the geometric standard deviation of a
                        vector
normalize,NanoStringGeoMxSet-method
                        normalize
plotConcordance         Generate concordance figure of targets based on
                        user provided factors
plotNormFactorConcordance
                        Generate concordance figure of normalization
                        factors based on user provided factors
qcProteinSignal         Generate Protein QC signal boxplot figure
qcProteinSignalNames    Generate list of proteins ordered by SNR
readDccFile             Read DCC File
readNanoStringGeoMxSet
                        Read 'NanoStringGeoMxSet'
readPKCFile             Read PKC File
setBackgroundQCFlags    Add background QC flags to NanoStringGeoMxSet
                        object protocol data
setBioProbeQCFlags      Add probe QC flags to NanoStringGeoMxSet object
                        feature data
setGeoMxQCFlags         Add GeoMx segment QC flags to
                        NanoStringGeoMxSet object protocol data
setQCFlags,NanoStringGeoMxSet-method
                        Add QC flags to feature and protocol data
                        simultaneously
setSegmentQCFlags       Add segment QC flags to protocol data
setSeqQCFlags           Add sequencing QC flags to NanoStringGeoMxSet
                        object protocol data
shiftCountsOne          Add one to all counts in an expression matrix
summarizeNegatives      Calculate negative probe summary stats
updateGeoMxSet          Update GeoMxSet object to current version
writeNanoStringGeoMxSet
                        write 'NanoStringGeoMxSet'
