Name Mode Size
figures 040000
MsExperiment.Rd 100644 15 kb
MsExperimentFiles.Rd 100644 2 kb
dbWriteSampleData.Rd 100644 3 kb
readMsExperiment.Rd 100644 2 kb
% Generated by roxygen2: do not edit by hand % Please edit documentation in R/MsExperiment-functions.R \name{readMsExperiment} \alias{readMsExperiment} \title{Import MS spectra data of an experiment} \usage{ readMsExperiment(spectraFiles = character(), sampleData = data.frame(), ...) } \arguments{ \item{spectraFiles}{\code{character} with the (absolute) file names of the MS data files that should be imported as a \code{\link[=Spectra]{Spectra()}} object.} \item{sampleData}{\code{data.frame} or \code{DataFrame} with the sample annotations. Each row is expected to contain annotations for one file (sample). The order of the data frame's rows is expected to match the order of the provided files (with parameter \code{spectraFiles}).} \item{...}{additional parameters for the \code{\link[=Spectra]{Spectra()}} call to import the data.} } \value{ \code{MsExperiment}. } \description{ Read/import MS spectra data of an experiment from the respective (raw) data files into an \code{\link[=MsExperiment]{MsExperiment()}} object. Files provided with the \code{spectraFiles} parameter are imported as a \code{Spectra} object and each file is automatically \emph{linked} to rows (samples) of a \code{sampleData} data frame (if provided). } \examples{ ## Define the files of the experiment to import fls <- c(system.file("microtofq/MM14.mzML", package = "msdata"), system.file("microtofq/MM8.mzML", package = "msdata")) ## Define a data frame with some sample annotations ann <- data.frame( injection_index = 1:2, sample_id = c("MM14", "MM8")) ## Import the data library(MsExperiment) mse <- readMsExperiment(spectraFiles = fls, ann) mse ## Access the spectra data spectra(mse) ## Access the sample annotations sampleData(mse) ## Import the data reading all MS spectra directly into memory mse <- readMsExperiment(spectraFiles = fls, ann, backend = Spectra::MsBackendMemory()) mse } \author{ Johannes Rainer }