writeNanoStringGeoMxSet {GeomxTools} | R Documentation |
Take an instance of class NanoStringGeoMxSet
and write
NanoString GeoMx Digital Count Conversion (DCC) data.
writeNanoStringGeoMxSet(x, dir = getwd())
x |
A NanoStringGeoMxSet object. |
dir |
A directory path to save all the DCC files. |
Zhi Yang & Nicole Ortogero
# 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)