# NanoString GeoMx Tools

## Documentation for package ‘GeomxTools’ version 3.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

aggregateCounts | Aggregate probe counts to target level for feature data
analyte | Class to Contain NanoString Spatial Expression Level Assays
analyte-method | Class to Contain NanoString Spatial Expression Level Assays
as.Seurat | Convert GeoMxSet Object to SeuratObject
as.Seurat.NanoStringGeoMxSet | Convert GeoMxSet Object to SeuratObject
as.SpatialExperiment | Convert Object to SpatialExperiment
as.SpatialExperiment.NanoStringGeoMxSet | Convert Object to SpatialExperiment
checkQCFlags | Check QC Flags in the GeoMxSet and removes the probe or sample from the object
checkQCFlags-method | checkQCFlags
class:NanoStringGeoMxSet | Class to Contain NanoString Spatial Expression Level Assays
coerce-method | Class to Contain NanoString Spatial Expression Level Assays
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
design-method | Class to Contain NanoString Spatial Expression Level Assays
design<--method | Class to Contain NanoString Spatial Expression Level Assays
dimLabels-method | Class to Contain NanoString Spatial Expression Level Assays
dimLabels<--method | Class to Contain NanoString Spatial Expression Level Assays
featureType | Class to Contain NanoString Spatial Expression Level Assays
featureType-method | Class to Contain NanoString Spatial Expression Level Assays
featureType<- | Class to Contain NanoString Spatial Expression Level Assays
featureType<--method | Class to Contain NanoString Spatial Expression Level Assays
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
NanoStringGeoMxSet | Class to Contain NanoString Spatial Expression Level Assays
NanoStringGeoMxSet-class | Class to Contain NanoString Spatial Expression Level Assays
NanoStringGeoMxSet-method | Class to Contain NanoString Spatial Expression Level Assays
ngeoMean | Get the geometric mean of a vector
ngeoSD | Get the geometric standard deviation of a vector
normalize-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
sData | Class to Contain NanoString Spatial Expression Level Assays
sData-method | Class to Contain NanoString Spatial Expression Level Assays
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-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
show-method | Class to Contain NanoString Spatial Expression Level Assays
signatureGroups | Class to Contain NanoString Spatial Expression Level Assays
signatureGroups-method | Class to Contain NanoString Spatial Expression Level Assays
signatures | Class to Contain NanoString Spatial Expression Level Assays
signatures-method | Class to Contain NanoString Spatial Expression Level Assays
signatures<- | Class to Contain NanoString Spatial Expression Level Assays
signatures<--method | Class to Contain NanoString Spatial Expression Level Assays
signatureScores | Class to Contain NanoString Spatial Expression Level Assays
signatureScores-method | Class to Contain NanoString Spatial Expression Level Assays
summarizeNegatives | Calculate negative probe summary stats
svarLabels | Class to Contain NanoString Spatial Expression Level Assays
svarLabels-method | Class to Contain NanoString Spatial Expression Level Assays
updateGeoMxSet | Update GeoMxSet object to current version
updateObject-method | Class to Contain NanoString Spatial Expression Level Assays
writeNanoStringGeoMxSet | write 'NanoStringGeoMxSet'