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NanoStringQCPro (version 1.4.0)

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

Description

NanoStringQCPro provides a set of quality metrics that can be used to assess the quality of NanoString mRNA gene expression data -- i.e. to identify outlier probes and outlier samples. It also provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and an easily sharable html quality control output.

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Version

Version

1.4.0

License

Artistic-2.0

Maintainer

Robert Ziman

Last Published

February 15th, 2017

Functions in NanoStringQCPro (1.4.0)

flagSamplesCtrl,RccSet-method

flagSamplesCtrl
example_rccSet

NanoStringQCPro example dataset
contentNorm,RccSet-method

Content normalization
addQCFlags,RccSet-method

Add sample QC flags to an rccSet
checkRccSet,RccSet-method

Check an RccSet
countsInBlankSamples_verticalPlot

Plot counts in blank samples (vertical orientation)
readRcc

Read an .RCC file
nSolverCsv.to.pdata_fdata_adata

nSolverCsv.to.pdata_fdata_fdata
sampleClustering,RccSet-method

Clustering by sample correlation
flagSamplesCount,RccSet-method

flagSamplesCount
negCtrlsPairs,RccSet-method

negCtrlsPairs
newRccSet

Create a new RccSet object
preprocRccSet,RccSet-method

Preprocess an RccSet
presAbsCall,RccSet-method

Presence/absence call
zfacFun

zfacFun
NanoStringQCPro

NanoStringQCPro
makeQCReport,RccSet-method

Make NanoString QC report
negCtrlsByLane_verticalPlot

Plot of negative controls by lane (vertical orientation)
previewPNG

Create a preview of a PNG
assessHousekeeping,RccSet-method

assessHousekeeping
colByCovar

colByCovar
addCodesetAnnotation,RccSet-method

Add NanoString codeset annotation to an RccSet
ctrlsZprimePlot,RccSet-method

ctrlsZprimePlot
RccSet

RccSet constructor methods
nSolverBackground,RccSet-method

nSolver Analysis Software background estimation
scatterPair

scatterPair
ctrlsOverviewPlot,RccSet-method

ctrlsOverviewPlot
colByFun

colByFun
posCtrlNorm,RccSet-method

Positive control normalization
readRccBatch

Read RCC files
getBlankLabel,RccSet-method

Get the SampleType value that indicates blank samples
getBackground,RccSet-method

Get background estimates for a NanoString RccSet
readCdrDesignData

Read .CSV containing CDR 'Design Data' extract
negCtrlsPlot,RccSet-method

negCtrlsPlot
posNormFactPlot,RccSet-method

posNormFactPlot
posSlopePlot,RccSet-method

posSlopePlot
allSumPlot,RccSet-method

allSumPlot
posSumVsAllSumPlot,RccSet-method

posSumVsAllSumPlot
bdPlot,RccSet-method

Binding density plot
myCols

myCols
copyRccSet,RccSet-method

Deep-copy a NanoString RccSet
fovPlot,RccSet-method

Fields of view (FOV) plot
flagSamplesTech,RccSet-method

flagSamplesTech
lodPlot,RccSet-method

lodPlot
negCtrlsByLane,RccSet-method

negCtrlsByLane
panelCor

panelCor
pdata_fdata_adata.to.rccSet

pdata_fdata_adata.to.rccSet
densityPlot

densityPlot
getSpikeInInput

getSpikeInInput
lodAssess,RccSet-method

lodAssess
RccSet-class

RccSet class, derived from ExpressionSet
buildCodesetAnnotation

Build NanoString codeset annotation
cutoffByMMAD

cutoffByMMAD
iqrPlot,RccSet-method

iqrPlot
pcaPlot

pcaPlot
rccFiles.to.pdata_fdata_adata

rccFiles.to.pdata_fdata_adata
dCoVar

dCoVar
geneClustering

Gene clustering heatmap
readRccCollectorToolExport

Read RCC Collector Tool Export
subtractBackground,RccSet-method

Subtract background estimates for a NanoString RccSet
cutoffByVar

cutoffByVar
readRlf

Read RLF file
posR2Plot,RccSet-method

posR2Plot
posRatioPlot,RccSet-method

posRatioPlot