readNanoStringGeoMxSet {GeomxTools}R Documentation

Read 'NanoStringGeoMxSet'

Description

Create an instance of class NanoStringGeoMxSet by reading data from NanoString GeoMx Digital Count Conversion (DCC) data.

Usage

readNanoStringGeoMxSet(dccFiles, pkcFiles, phenoDataFile, 
                     phenoDataSheet, phenoDataDccColName = "Sample_ID",
                     phenoDataColPrefix = "", protocolDataColNames = NULL,
                     experimentDataColNames = NULL, ...)

Arguments

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 phenoDataFile.

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 phenoDataFile containing data about the experimental protocol or sequencing data.

experimentDataColNames

Character list of column names from phenoDataFile containing data about the experiment's meta-data.

...

Optional parameters to pass to readxl::read_xlsx function for annotation read in

Value

An instance of the NanoStringGeoMxSet class.

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
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)

[Package GeomxTools version 2.0.0 Index]