Quality metrics and data processing methods for NanoString mRNA
gene expression data
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Documentation for package ‘NanoStringQCPro’ version 1.31.0
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 |