NanoStringGeoMxSet-class: Class to Contain NanoString Spatial Expression Level Assays

In Nanostring-Biostats/GeomxTools: NanoString GeoMx Tools

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",
                 analyte="RNA",
                 ...)

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
analyte	A character string indicating if features are "RNA" or "Protein"
...	Additional arguments for ExpressionSet.

Value

An S4 class containing data from a NanoString GeoMx experiment

Updating

Objects can be updated to current version using updateGeoMxSet(object)

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.

analyte(object)

extracts the analyte of the object.

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)
analyte(dccSet)

# Accessing number of samples and features
dim(dccSet)

Nanostring-Biostats/GeomxTools documentation built on Sept. 24, 2024, 4:51 p.m.