NanoStringGeoMxSet-class {GeomxTools}

R Documentation

Class to Contain NanoString Spatial Expression Level Assays

Description

The NanoStringGeoMxSet class extends the ExpressionSet class for NanoString GeoMx Digital Count Conversion (DCC) data.

Usage

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",
                 ...)

Arguments

assayData	A matrix or environment containing the DCCs.
phenoData	An AnnotatedDataFrame containing the phenotypic data of areas of interest.
featureData	An AnnotatedDataFrame containing target information; target name, accession number, functional groups, etc.
experimentData	An optional MIAME instance with meta-data about the experiment.
annotation	A character string for the PKC file(s).
protocolData	An AnnotatedDataFrame containing meta-data about the protocol and sequencing; columns could include "FileVersion", "SoftwareVersion", "Date", "Plate_ID", "Well", "SeqSetId", "trimGaloreOpts", "flash2Opts", "umiExtractOpts", "boxtie2Opts", "Raw", "Trimmed", "Stitched", "Aligned", "umiQ30", "rtsQ30".
dimLabels	A character vector of length 2 that provides the column names to use as labels for the features and samples respectively in the autoplot method.
signatures	An optional SignatureSet object containing signature definitions.
design	An optional one-sided formula representing the experimental design based on columns from phenoData
featureType	A character string indicating if features are on "Probe" or "Target" level
...	Additional arguments for ExpressionSet.

Value

An S4 class containing data from a NanoString GeoMx experiment

Accessing

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.

Author(s)

Zhi Yang & Nicole Ortogero

See Also

readNanoStringGeoMxSet, ExpressionSet

Examples

# 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)

---