# NanoString nCounter Tools

## Documentation for package ‘NanoStringNCTools’ version 1.20.0

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

## Help Pages

A C D E F G H L M N P R S T U V W misc

## -- A --

assayDataApply | Class to Contain NanoString Expression Level Assays
assayDataApply-method | Class to Contain NanoString Expression Level Assays
autoplot | Plot NanoStringRccSet Data
autoplot.NanoStringRccSet | Plot NanoStringRccSet Data

## -- C --

class:NanoStringRccSet | Class to Contain NanoString Expression Level Assays
class:SignatureSet | Class to Contain Signature Definitions
coerce-method | Class to Contain NanoString Expression Level Assays
controlSubset | Class to Contain NanoString Expression Level Assays
controlSubset-method | Class to Contain NanoString Expression Level Assays

## -- D --

design-method | Class to Contain NanoString Expression Level Assays
design<--method | Class to Contain NanoString Expression Level Assays
dimLabels-method | Class to Contain NanoString Expression Level Assays
dimLabels<--method | Class to Contain NanoString Expression Level Assays

## -- E --

endogenousSubset | Class to Contain NanoString Expression Level Assays
endogenousSubset-method | Class to Contain NanoString Expression Level Assays
esBy | Class to Contain NanoString Expression Level Assays
esBy-method | Class to Contain NanoString Expression Level Assays

## -- F --

fAbove | Convenience Functions for Assay Data Element Sweep Operations
fAtLeast | Convenience Functions for Assay Data Element Sweep Operations
fAtMost | Convenience Functions for Assay Data Element Sweep Operations
fBelow | Convenience Functions for Assay Data Element Sweep Operations
fCenter | Convenience Functions for Assay Data Element Sweep Operations
fIntCenter | Convenience Functions for Assay Data Element Sweep Operations
fIntScale | Convenience Functions for Assay Data Element Sweep Operations
fIntThresh | Convenience Functions for Assay Data Element Sweep Operations
fScale | Convenience Functions for Assay Data Element Sweep Operations
fThresh | Convenience Functions for Assay Data Element Sweep Operations

## -- G --

geom_beeswarm_interactive | Geometry for Interactive Bee Swarm Points
getSigFuncs | Class to Contain Signature Definitions
getSigFuncs-method | Class to Contain Signature Definitions
ggplot.NanoStringRccSet | Class to Contain NanoString Expression Level Assays
groups | Class to Contain Signature Definitions
groups-method | Class to Contain Signature Definitions
groups<- | Class to Contain Signature Definitions
groups<--method | Class to Contain Signature Definitions

## -- H --

housekeepingSubset | Class to Contain NanoString Expression Level Assays
housekeepingSubset-method | Class to Contain NanoString Expression Level Assays

## -- L --

length-method | Class to Contain Signature Definitions
lengths-method | Class to Contain Signature Definitions
log2t | Logarithm With Thresholding
logt | Logarithm With Thresholding

## -- M --

munge | Class to Contain NanoString Expression Level Assays
munge-method | Class to Contain NanoString Expression Level Assays

## -- N --

names-method | Class to Contain Signature Definitions
NanoStringRccSet | Class to Contain NanoString Expression Level Assays
NanoStringRccSet-autoplot | Plot NanoStringRccSet Data
NanoStringRccSet-class | Class to Contain NanoString Expression Level Assays
NanoStringRccSet-method | Class to Contain NanoString Expression Level Assays
negativeControlSubset | Class to Contain NanoString Expression Level Assays
negativeControlSubset-method | Class to Contain NanoString Expression Level Assays
nonControlSubset | Class to Contain NanoString Expression Level Assays
nonControlSubset-method | Class to Contain NanoString Expression Level Assays
normalize | Normalize RCCSet
normalize-method | Class to Contain NanoString Expression Level Assays

## -- P --

positiveControlSubset | Class to Contain NanoString Expression Level Assays
positiveControlSubset-method | Class to Contain NanoString Expression Level Assays

## -- R --

readNanoStringRccSet | Read 'NanoStringRccSet'
readRccFile | Read RCC File
readRlfFile | Read RLF File

## -- S --

sAbove | Convenience Functions for Assay Data Element Sweep Operations
sAtLeast | Convenience Functions for Assay Data Element Sweep Operations
sAtMost | Convenience Functions for Assay Data Element Sweep Operations
sBelow | Convenience Functions for Assay Data Element Sweep Operations
sCenter | Convenience Functions for Assay Data Element Sweep Operations
sData | Class to Contain NanoString Expression Level Assays
sData-method | Class to Contain NanoString Expression Level Assays
setQCFlags | Set flags for QC of the assayData in a NanoStringRccSet.
setQCFlags-method | Class to Contain NanoString Expression Level Assays
setSignatureFuncs<- | Class to Contain NanoString Expression Level Assays
setSignatureFuncs<--method | Class to Contain NanoString Expression Level Assays
setSignatureGroups<- | Class to Contain NanoString Expression Level Assays
setSignatureGroups<--method | Class to Contain NanoString Expression Level Assays
show-method | Class to Contain NanoString Expression Level Assays
show-method | Class to Contain Signature Definitions
signatureFuncs | Class to Contain NanoString Expression Level Assays
signatureFuncs-method | Class to Contain NanoString Expression Level Assays
signatureGroups | Class to Contain NanoString Expression Level Assays
signatureGroups-method | Class to Contain NanoString Expression Level Assays
signatures | Class to Contain NanoString Expression Level Assays
signatures-method | Class to Contain NanoString Expression Level Assays
signatures<- | Class to Contain NanoString Expression Level Assays
signatures<--method | Class to Contain NanoString Expression Level Assays
signatureScores | Class to Contain NanoString Expression Level Assays
signatureScores-method | Class to Contain NanoString Expression Level Assays
signatureScoresApply | Class to Contain NanoString Expression Level Assays
signatureScoresApply-method | Class to Contain NanoString Expression Level Assays
SignatureSet | Class to Contain Signature Definitions
SignatureSet-class | Class to Contain Signature Definitions
signatureSubset | Class to Contain NanoString Expression Level Assays
signatureSubset-method | Class to Contain NanoString Expression Level Assays
sIntCenter | Convenience Functions for Assay Data Element Sweep Operations
sIntScale | Convenience Functions for Assay Data Element Sweep Operations
sIntThresh | Convenience Functions for Assay Data Element Sweep Operations
sScale | Convenience Functions for Assay Data Element Sweep Operations
sThresh | Convenience Functions for Assay Data Element Sweep Operations
subset-method | Class to Contain NanoString Expression Level Assays
summary-method | Class to Contain NanoString Expression Level Assays
svarLabels | Class to Contain NanoString Expression Level Assays
svarLabels-method | Class to Contain NanoString Expression Level Assays

## -- T --

transform-method | Class to Contain NanoString Expression Level Assays

## -- U --

update_geom_params | Class to Contain NanoString Expression Level Assays

## -- V --

version | Class to Contain Signature Definitions
version-method | Class to Contain Signature Definitions
version<- | Class to Contain Signature Definitions
version<--method | Class to Contain Signature Definitions

## -- W --

weights-method | Class to Contain Signature Definitions
weights<- | Class to Contain Signature Definitions
weights<--method | Class to Contain Signature Definitions
with-method | Class to Contain NanoString Expression Level Assays
writeNanoStringRccSet | Write NanoString Reporter Code Count (RCC) files

## -- misc --

[-method | Class to Contain NanoString Expression Level Assays