NanoStringExperiment-class: The NanoStringExperiment class

In Nanostring-Biostats/NanoStringExperiment: Base NanoString Experiment Class

The NanoStringExperiment class

Description

Class definition for the base NanoString experiment

Show method for NanoStringExperiment

Constructs NanoStringExperiment object based on assay data signature

Constructs NanoStringExperiment object if assay data missing

Constructs NanoStringExperiment object if assay data is a matrix

Usage

## S4 method for signature 'NanoStringExperiment'
show(object)

NanoStringExperiment(
  assayData,
  phenoData = Biobase::annotatedDataFrameFrom(assayData, byrow = FALSE),
  protocolData = Biobase::annotatedDataFrameFrom(assayData, byrow = FALSE),
  featureData = Biobase::annotatedDataFrameFrom(assayData, byrow = TRUE),
  experimentData = Biobase::MIAME(),
  annotation = character(),
  dimLabels = character(),
  signatures = NanoStringNCTools::SignatureSet(),
  design = NULL,
  ...
)

## S4 method for signature 'missing'
NanoStringExperiment(
  assayData,
  phenoData = Biobase::annotatedDataFrameFrom(assayData, byrow = FALSE),
  protocolData = Biobase::annotatedDataFrameFrom(assayData, byrow = FALSE),
  featureData = Biobase::annotatedDataFrameFrom(assayData, byrow = TRUE),
  experimentData = Biobase::MIAME(),
  annotation = character(),
  dimLabels = character(),
  signatures = NanoStringNCTools::SignatureSet(),
  design = NULL,
  ...
)

## S4 method for signature 'matrix'
NanoStringExperiment(
  assayData,
  phenoData = Biobase::annotatedDataFrameFrom(assayData, byrow = FALSE),
  protocolData = Biobase::annotatedDataFrameFrom(assayData, byrow = FALSE),
  featureData = Biobase::annotatedDataFrameFrom(assayData, byrow = TRUE),
  experimentData = Biobase::MIAME(),
  annotation = character(),
  dimLabels = character(),
  signatures = NanoStringNCTools::SignatureSet(),
  design = NULL,
  ...
)

Arguments

object	NanoStringExperiment object
assayData	matrix of expression values
phenoData	AnnotatedDataFrame with phenotype metadata
protocolData	AnnotatedDataFrame with protocol metadata
featureData	AnnotatedDataFrame with feature metadata
experimentData	MIAME object
annotation	list of annotations used
dimLabels	list of key headers for row and column metadata
signatures	SignatureSet object
design	formula or NULL
...	parameters to pass

Value

NanoStringExperiment object

summary of NanoStringExperiment object

NanoStringExperiment object

NanoStringExperiment object

NanoStringExperiment object

Slots

.__classVersion__

version of class

assayData

expression matrix or NULL

annotation

character list of annotations used

dimLabels

character list of dimension labels

signatures

optional SignatureSet object

design

formula or NULL

Examples

data(exampleNSEData)
show(testExp)

data(exampleNSEData)
NanoStringExperiment(
    assayData = testAssayData,
    phenoData = testPhenoData,
    protocolData = testProtocolData,
    featureData = testFeatureData,
    experimentData = testExperimentData,
    annotation = testAnnotation,
    dimLabels = testDimLabels)

NanoStringExperiment()

data(exampleNSEData)
NanoStringExperiment(
    assayData = testAssayData,
    phenoData = testPhenoData,
    protocolData = testProtocolData,
    featureData = testFeatureData,
    experimentData = testExperimentData,
    annotation = testAnnotation,
    dimLabels = testDimLabels)

Nanostring-Biostats/NanoStringExperiment documentation built on April 28, 2022, 6:24 a.m.