importSpectra: Convert mass spectra from text files into 'MassSpectrum'...

In Japal/MALDIrppa: MALDI Mass Spectrometry Data Robust Pre-Processing and Analysis

Convert mass spectra from text files into MassSpectrum objects

Description

This function allows to import collections of mass spectra stored in individual text files into a list of MassSpectrum objects.

Usage

importSpectra(where = getwd())

Arguments

where

Path to the folder where the text files are stored (default: current working directory).

Details

This functions works with dat, csv or txt file types containing two columns: the first one referring to common m/z values and the second one to intensities (using single-space separator between both and no column names). It reads all the .dat, .csv or .txt files in the given folder (so unrelated files should better not be there) and creates a list of MassSpectrum objects. For importing data from more specialised file formats we refer the reader to the package MALDIquantForeign.

Value

A list of MassSpectrum objects.

Examples

# Create fake mass spectrometry data

s1 <- cbind(1:20, rlnorm(20))
s2 <- cbind(1:20, rlnorm(20))
s3 <- cbind(1:20, rlnorm(20))

# Save as csv files in temporary directory

path <- tempdir()

write.table(s1, file = file.path(path, "s1.csv"),
            row.names = FALSE, col.names = FALSE, sep=" ")
write.table(s2, file = file.path(path, "s2.csv"),
            row.names = FALSE, col.names = FALSE, sep=" ")
write.table(s3, file = file.path(path, "s3.csv"),
            row.names = FALSE, col.names = FALSE, sep=" ")

# Import files and arrange into a list of MassSpectrum objects

spectra <- importSpectra(where = path)

Japal/MALDIrppa documentation built on Jan. 31, 2024, 12:15 p.m.