A Parser for nmrML

Steffen Neumann (sneumannipb-halle.de), Luis Filipe de Figueiredo (Luis.deFigueiredoebi.ac.uk) Jie Hao (j.hao“imperial.ac.uk)

Introduction

The nmRIO package aims at providing a common interface to several NMR data formats.

Cool R packages for NMR processing are e.g. cite(Lewis09rNMRopensource) and cite(Hao12BATMANRpackage)

Example

A short example sequence to read data from a mass spectrometer. First open the file.

library(nmRIO)

## Loading required package: XML
## Loading required package: caTools

nmrMLfile <- system.file("examples/HMDB00005.nmrML", package = "nmRIO")

fid <- readNMRMLFID(nmrMLfile)

plot(Re(fid), type="l")

Luis: I also need to access the following parameters: spectral width (ideally in ppm but can work out the one in Hz) transmitter frequency. Later, for bruker files I also need the following data group delay, dsp firmware version

  tree <- xmlTreeParse(nmrMLfile)
  root <- xmlRoot(tree)
  ## Get required parameters from nmrML
  irradiationFrequency <- as.double(xmlAttrs(xmlElementsByTagName(root, "irradiationFrequency", recursive = TRUE)[[1]])["value"])

  sweepWidth <- as.double(xmlAttrs(xmlElementsByTagName(root, "sweepWidth", recursive = TRUE)[[1]])["value"])

  numberOfDataPoints <- as.integer(xmlAttrs(xmlElementsByTagName(root, "DirectDimensionParameterSet", recursive = TRUE)[[1]])["numberOfDataPoints"])

  irradiationFrequency

## [1] 599.4

  sweepWidth

## [1] 7200

  numberOfDataPoints

## [1] 57804

  spectrum <- Re(fft(fid, inverse=TRUE))

The rudimentary processing results in:

plot(spectrum, type="l")

## Mockup to write the spectrum back into the nmrML 
## as "processed data"

#b64string <- nmRIO:::binaryArrayEncode(spectrum, byteFormat="complex64", compression="gzip")

Future plans

A lot.

Session information

## R version 3.1.1 (2014-07-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] nmRIO_0.3    caTools_1.17 XML_3.98-1.1 knitr_1.6   
## 
## loaded via a namespace (and not attached):
## [1] bitops_1.0-6   evaluate_0.5.5 formatR_0.10   stringr_0.6.2 
## [5] tools_3.1.1