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


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Documentation for package ‘NanoStringQCPro’ version 1.19.0

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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