NanoStringGeoMxSet-class {GeomxTools} | R Documentation |
The NanoStringGeoMxSet
class extends the
ExpressionSet
class for NanoString GeoMx Digital Count Conversion
(DCC) data.
NanoStringGeoMxSet(assayData, phenoData=Biobase::annotatedDataFrameFrom(assayData, byrow=FALSE), featureData=Biobase::annotatedDataFrameFrom(assayData, byrow=TRUE), experimentData=Biobase::MIAME(), annotation=character(), protocolData=Biobase::annotatedDataFrameFrom(assayData, byrow=FALSE), dimLabels=c("TargetName", "SampleID"), signatures=SignatureSet(), design=NULL, featureType="Probe", ...)
assayData |
A |
phenoData |
An |
featureData |
An |
experimentData |
An optional |
annotation |
A |
protocolData |
An |
dimLabels |
A |
signatures |
An optional |
design |
An optional one-sided formula representing the experimental
design based on columns from |
featureType |
A |
... |
Additional arguments for |
An S4 class containing data from a NanoString GeoMx experiment
In addition to the standard ExpressionSet
accessor
methods, NanoStringGeoMxSet
objects have the following:
sData(object)
: extracts the data.frame
containing the
sample data, cbind(pData(object), pData(protocolData(object)))
.
svarLabels(object)
: extracts the sample data column names,
c(varLabels(object), varLabels(protocolData(object)))
.
dimLabels(object)
: extracts the column names to use as labels
for the features and samples.
dimLabels(object) <- value
: replaces the dimLabels
of
the object
.
featureType(object)
: extracts the featureType
of the object
.
featureType(object) <- value
: replaces the featureType
of the object
.
signatures(object)
: extracts the SignatureSet
of the object
.
signatures(object) <- value
: replaces the
SignatureSet
of the object
.
signatureScores(object, elt="exprs")
: extracts the matrix
of computed signature scores.
design(object)
: extracts the one-sided formula representing
the experimental design based on columns from
phenoData
.
design(object) <- value
: replaces the one-sided formula
representing the experimental design based on columns from
phenoData
.
signatureGroups(object)
: extract the groups of
SignatureSet
.
signatureGroups(object) <- value
: replaces the groups of
SignatureSet
.
Zhi Yang & Nicole Ortogero
readNanoStringGeoMxSet
,
ExpressionSet
# Create NanoStringGeoMxSet from data files datadir <- system.file("extdata", "DSP_NGS_Example_Data", package="GeomxTools") dccFiles <- dir(datadir, pattern=".dcc$", full.names=TRUE) pkc <- unzip(zipfile = file.path(datadir, "/pkcs.zip")) sampleAnnotationFile <- file.path(datadir, "annotations.xlsx") dccFileColumn <- "Sample_ID" dccSet <- readNanoStringGeoMxSet(dccFiles=dccFiles, pkcFiles=pkc, phenoDataFile=sampleAnnotationFile, phenoDataSheet="CW005", phenoDataDccColName=dccFileColumn, protocolDataColNames=c("aoi", "cell_line", "roi_rep", "pool_rep", "slide_rep"), experimentDataColNames="panel", phenoDataColPrefix="") # Accessing sample data and column names head(sData(dccSet)) svarLabels(dccSet) featureType(dccSet) # Accessing number of samples and features dim(dccSet)