readNanoStringGeoMxSet {GeomxTools} | R Documentation

## Read 'NanoStringGeoMxSet'

### Description

Create an instance of class `NanoStringGeoMxSet` by reading data from NanoString GeoMx Digital Count Conversion (DCC) data.

### Usage

    readNanoStringGeoMxSet(dccFiles, pkcFiles, phenoDataFile,
                         phenoDataSheet, phenoDataDccColName = "Sample_ID",
                         phenoDataColPrefix = "", protocolDataColNames = NULL,
                         experimentDataColNames = NULL, ...)

### Arguments

`dccFiles` | A character vector containing the paths to the DCC files.
`pkcFiles` | An optional character string representing the path to the corresponding PKC file.
`phenoDataFile` | An optional character string representing the path to the corresponding phenotypic excel data file.
`phenoDataSheet` | An optional character string representing the excel sheet name containing the phenotypic data.
`phenoDataDccColName` | Character string identifying unique sample identifier column in `phenoDataFile`.
`phenoDataColPrefix` | An optional prefix to add to the phenoData column names to distinguish them from the names of assayData matrices, featureData columns, and protocolData columns.
`protocolDataColNames` | Character list of column names from `phenoDataFile` containing data about the experimental protocol or sequencing data.
`experimentDataColNames` | Character list of column names from `phenoDataFile` containing data about the experiment's meta-data.
`...` | Optional parameters to pass to `readxl::read_xlsx` function for annotation read in

### Value

An instance of the `NanoStringGeoMxSet` class.

### Author(s)

Zhi Yang & Nicole Ortogero

### See Also

`NanoStringGeoMxSet`

### Examples

    # Data file paths
    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="")

    # All data
    dccSet <- readNanoStringGeoMxSet(dccFiles, pkcFile = pkc,
                                     phenoDataFile = sampleAnnotationFile,
                                     phenoDataSheet="CW005")
    varLabels(dccSet)

    # All data with phenoData prefix
    dccSetPhenoPrefix <- readNanoStringGeoMxSet(dccFiles,
                                    pkcFile = pkc,
                                    phenoDataFile = sampleAnnotationFile,
                                    phenoDataSheet="CW005",
                                    phenoDataColPrefix = "PHENO_")
    varLabels(dccSetPhenoPrefix)

[Package GeomxTools version 2.0.0 Index]