NanoString GeoMx Tools

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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'