NanoString nCounter Tools

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Documentation for package ‘NanoStringNCTools’ version 1.10.1

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

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