View source: R/writeNanoStringGeoMxSet.R
writeNanoStringGeoMxSet | 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
NanoStringGeoMxSet
# 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)
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