writeNanoStringGeoMxSet {GeomxTools} | R Documentation

## write 'NanoStringGeoMxSet'

### Description

Take an instance of class `NanoStringGeoMxSet` and write NanoString GeoMx Digital Count Conversion (DCC) data.

### Usage

    writeNanoStringGeoMxSet(x, dir = getwd())

### Arguments

`x` | A NanoStringGeoMxSet object.
`dir` | A directory path to save all the DCC files.

### 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
    writeNanoStringGeoMxSet(dccSet)

[Package GeomxTools version 2.0.0 Index]