README.md

In wilsontom/rawReadeR: Read Thermo .RAW files in R

rawReadeR

read Thermo .RAW data into R

What is rawReadeR ?

rawReadeR is an R/C++ API to the MSFileReader.dll. rawReadeR allows for m/z profiles and scan header data to be extracted from .RAW files without the need for manual extraction using Xcalibur or conversion to a more universal format (.mzML, .mZXML, etc...)

Installation

N.B rawReadeR can only be installed on a Windows Operating System. Microsoft Visual Studio also needs to be installed to allow for compilation of .cpp files.

Step 1

• Download the MSFileReader
• The MSFileReader filepath needs to be C:\Thermo\MSFileReader.XRawfile2.dll
• The .dll can then be registered using the following command from a Command Prompt with Administrator privileges regsvr32 C:\Thermo\MSFileReader.XRawfile2.dll

Step 2

• Clone the repository

git clone https://github.com/wilsontom/rawReadeR

Step 3

To prevent having to distibute compied executables with the package, these need to be compiled prior to package installation. Start a new R session and enter the following;

setwd("rawReadeR")
options(VSPATH = "<path_to_visual_studio_vsvars32.bat>")
source("rawReadeR/R/compileAll.R")
compileAll(getwd())

Step 4

Finally, build and install.

R CMD build RawReadeR
R CMD INSTALL RawReadeR_0.1.0_tar.gz

Step 5

To check everything has compiled and installed ok...

library(rawReadeR)
testPackage(scans = c(1:10)

Acknowledgments

This package was inspired by a similar effort using MATLAB and the mex complier. Also, Galaxy-M contains a excellent Python parser for MSfilereader which was helpful during development of this package

wilsontom/rawReadeR documentation built on May 4, 2019, 6:31 a.m.