# Quality metrics and data processing methods for NanoString mRNA gene expression data

## Documentation for package ‘NanoStringQCPro’ version 1.26.0

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

## Help Pages

A B C D E F G I L M N P R S Z misc

NanoStringQCPro-package | NanoStringQCPro

## -- A --

addCodesetAnnotation | Add NanoString codeset annotation to an RccSet
addCodesetAnnotation-method | Add NanoString codeset annotation to an RccSet
addQCFlags | Add sample QC flags to an rccSet
addQCFlags-method | Add sample QC flags to an rccSet
allSumPlot | allSumPlot
allSumPlot-method | allSumPlot
assessHousekeeping | assessHousekeeping
assessHousekeeping-method | assessHousekeeping

## -- B --

bdPlot | Binding density plot
bdPlot-method | Binding density plot
buildCodesetAnnotation | Build NanoString codeset annotation

## -- C --

checkRccSet | Check an RccSet
checkRccSet-method | Check an RccSet
colByCovar | colByCovar
colByFun | colByFun
contentNorm | Content normalization
contentNorm-method | Content normalization
copyRccSet | Deep-copy a NanoString RccSet
copyRccSet-method | Deep-copy a NanoString RccSet
countsInBlankSamples_verticalPlot | Plot counts in blank samples (vertical orientation)
ctrlsOverviewPlot | ctrlsOverviewPlot
ctrlsOverviewPlot-method | ctrlsOverviewPlot
ctrlsZprimePlot | ctrlsZprimePlot
ctrlsZprimePlot-method | ctrlsZprimePlot
cutoffByMMAD | cutoffByMMAD
cutoffByVar | cutoffByVar

## -- D --

dCoVar | dCoVar
densityPlot | densityPlot

## -- E --

example_rccSet | NanoStringQCPro example dataset

## -- F --

flagSamplesCount | flagSamplesCount
flagSamplesCount-method | flagSamplesCount
flagSamplesCtrl | flagSamplesCtrl
flagSamplesCtrl-method | flagSamplesCtrl
flagSamplesTech | flagSamplesTech
flagSamplesTech-method | flagSamplesTech
fovPlot | Fields of view (FOV) plot
fovPlot-method | Fields of view (FOV) plot

## -- G --

geneClustering | Gene clustering heatmap
getBackground | Get background estimates for a NanoString RccSet
getBackground-method | Get background estimates for a NanoString RccSet
getBlankLabel | Get the SampleType value that indicates blank samples
getBlankLabel-method | Get the SampleType value that indicates blank samples
getSpikeInInput | getSpikeInInput

## -- I --

iqrPlot | iqrPlot
iqrPlot-method | iqrPlot

## -- L --

lodAssess | lodAssess
lodAssess-method | lodAssess
lodPlot | lodPlot
lodPlot-method | lodPlot

## -- M --

makeQCReport | Make NanoString QC report
makeQCReport-method | Make NanoString QC report
myCols | myCols

## -- N --

NanoStringQCPro | NanoStringQCPro
negCtrlsByLane | negCtrlsByLane
negCtrlsByLane-method | negCtrlsByLane
negCtrlsByLane_verticalPlot | Plot of negative controls by lane (vertical orientation)
negCtrlsPairs | negCtrlsPairs
negCtrlsPairs-method | negCtrlsPairs
negCtrlsPlot | negCtrlsPlot
negCtrlsPlot-method | negCtrlsPlot
newRccSet | Create a new RccSet object
nSolverBackground | nSolver Analysis Software background estimation
nSolverBackground-method | nSolver Analysis Software background estimation
nSolverCsv.to.pdata_fdata_adata | nSolverCsv.to.pdata_fdata_fdata

## -- P --

panelCor | panelCor
pcaPlot | pcaPlot
pdata_fdata_adata.to.rccSet | pdata_fdata_adata.to.rccSet
posCtrlNorm | Positive control normalization
posCtrlNorm-method | Positive control normalization
posNormFactPlot | posNormFactPlot
posNormFactPlot-method | posNormFactPlot
posR2Plot | posR2Plot
posR2Plot-method | posR2Plot
posRatioPlot | posRatioPlot
posRatioPlot-method | posRatioPlot
posSlopePlot | posSlopePlot
posSlopePlot-method | posSlopePlot
posSumVsAllSumPlot | posSumVsAllSumPlot
posSumVsAllSumPlot-method | posSumVsAllSumPlot
preprocRccSet | Preprocess an RccSet
preprocRccSet-method | Preprocess an RccSet
presAbsCall | Presence/absence call
presAbsCall-method | Presence/absence call
previewPNG | Create a preview of a PNG

## -- R --

rccFiles.to.pdata_fdata_adata | rccFiles.to.pdata_fdata_adata
RccSet | RccSet constructor methods
RccSet-class | RccSet class, derived from ExpressionSet
RccSet-method | RccSet constructor methods
readCdrDesignData | Read .CSV containing CDR 'Design Data' extract
readRcc | Read an .RCC file
readRccBatch | Read RCC files
readRccCollectorToolExport | Read RCC Collector Tool Export
readRlf | Read RLF file

## -- S --

sampleClustering | Clustering by sample correlation
sampleClustering-method | Clustering by sample correlation
scatterPair | scatterPair
subtractBackground | Subtract background estimates for a NanoString RccSet
subtractBackground-method | Subtract background estimates for a NanoString RccSet

## -- Z --

zfacFun | zfacFun

## -- misc --

.RccSet | RccSet class, derived from ExpressionSet