writeNanoStringGeoMxSet: write 'NanoStringGeoMxSet'

In Nanostring-Biostats/GeomxTools: NanoString GeoMx Tools

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)

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