readNanoStringRccSet: Read 'NanoStringRccSet'

In Nanostring-Biostats/NanoStringNCTools: NanoString nCounter Tools

Read 'NanoStringRccSet'

Description

Create an instance of class NanoStringRccSet by reading data from NanoString Reporter Code Count (RCC) files.

Usage

readNanoStringRccSet(rccFiles, rlfFile = NULL,
                     phenoDataFile = NULL,
                     phenoDataRccColName = "^RCC",
                     phenoDataColPrefix = "")

Arguments

rccFiles	A character vector containing the paths to the RCC files.
rlfFile	An optional character string representing the path to the corresponding RLF file.
phenoDataFile	An optional character string representing the path to the corresponding phenotypic csv data file.
phenoDataRccColName	The regular expression that specifies the RCC column in the 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.

Value

An instance of the NanoStringRccSet class.

Author(s)

Patrick Aboyoun

See Also

NanoStringRccSet, writeNanoStringRccSet

Examples

# Data file paths
datadir <- system.file("extdata", "3D_Bio_Example_Data",
                       package = "NanoStringNCTools")
rccs <- dir(datadir, pattern = "SKMEL.*\\.RCC$", full.names = TRUE)
rlf <- file.path(datadir, "3D_SolidTumor_Sig.rlf")
pheno <- file.path(datadir, "3D_SolidTumor_PhenoData.csv")

# Just RCC data
solidTumorNoRlfPheno <- readNanoStringRccSet(rccs)
varLabels(solidTumorNoRlfPheno)
fvarLabels(solidTumorNoRlfPheno)

# RCC and RLF data
solidTumorNoPheno <- readNanoStringRccSet(rccs, rlfFile = rlf)
setdiff(fvarLabels(solidTumorNoPheno), fvarLabels(solidTumorNoRlfPheno))

# All data
solidTumor <-
  readNanoStringRccSet(rccs, rlfFile = rlf, phenoDataFile = pheno)
varLabels(solidTumor)
design(solidTumor) <- ~ BRAFGenotype + Treatment

# All data with phenoData prefix
solidTumorPhenoPrefix <-
  readNanoStringRccSet(rccs, rlfFile = rlf, phenoDataFile = pheno,
                       phenoDataColPrefix = "PHENO_")
varLabels(solidTumorPhenoPrefix)
design(solidTumorPhenoPrefix) <- ~ PHENO_BRAFGenotype + PHENO_Treatment

Nanostring-Biostats/NanoStringNCTools documentation built on Dec. 18, 2024, 1:24 a.m.