MALDIrppa (version 1.1.0-2)

writeMetadata: Write metadata in different formats

Description

This function is simply a wrapper to write the metadata associated with a collection of mass spectra into a file in either the R or csv format.

Usage

writeMetadata(x, filename = "Metadata", format = c("R", "csv"), ...)

Value

No return value, file in selected format created on destination folder.

Arguments

x

Metadata in any sensible data format, preferably matrix or data.frame.

filename

A character string specifying a name for the destination file (filename extension not required).

format

One of R (default .RData file) or text (comma-separated .csv file).

...

Other arguments.

Details

It uses either save or write.table to store the metadata. Check these functions for adequate data formats.

Examples

# Load example data

data(spectra) # list of MassSpectra class objects
data(type)    # metadata

# Some pre-processing

sc.spectra <- screenSpectra(spectra, meta = type)

spectra <- sc.spectra$fspectra # filtered spectra
type <- sc.spectra$fmeta # filtered metadata

spectra <- transformIntensity(spectra, method = "sqrt")
spectra <- wavSmoothing(spectra)
spectra <- removeBaseline(spectra)
peaks <- detectPeaks(spectra)
peaks <- alignPeaks(peaks, minFreq = 0.8)

# Intensity matrix

int <- intensityMatrix(peaks)

# Save resulting data in R format (to a temporary location as an example)
# \donttest{
writeIntensity(int, filename = file.path(tempdir(),"MyintMatrix"))
writeMetadata(type, filename = file.path(tempdir(),"MyMetadata"))
# }
# Save resulting data in csv format (to a temporary location as an example)
# \donttest{
writeIntensity(int, filename = file.path(tempdir(),"MyintMatrix"),
               format = "csv")
writeMetadata(type, filename = file.path(tempdir(),"MyMetadata"),
               format = "csv")
# }