readNanoStringRccSet {NanoStringNCTools} | R Documentation |
Create an instance of class NanoStringRccSet
by reading
data from NanoString Reporter Code Count (RCC) files.
readNanoStringRccSet(rccFiles, rlfFile = NULL, phenoDataFile = NULL, phenoDataRccColName = "^RCC", phenoDataColPrefix = "")
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 |
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. |
An instance of the NanoStringRccSet
class.
Patrick Aboyoun
NanoStringRccSet
, writeNanoStringRccSet
# 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