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)

[Package GeomxTools version 2.0.0 Index]