readNanoStringGeomxSet {GeomxTools} | R Documentation |
Create an instance of class NanoStringGeomxSet
by reading
data from NanoString GeoMx Digital Count Conversion (DCC) data.
readNanoStringGeomxSet(dccFiles, pkcFiles, phenoDataFile, phenoDataSheet, phenoDataDccColName = "Sample_ID", phenoDataColPrefix = "", protocolDataColNames = c("slide name"), experimentDataColNames = c("panel"))
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 |
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 |
experimentDataColNames |
Character list of column names from |
An instance of the NanoStringGeomxSet
class.
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 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)