README.md

Rnmr1D

Rnmr1D is the main module in the NMRProcFlow web application (http://nmrprocflow.org) concerning the NMR spectra processing.

• Inside NMRProcFlow, Rnmr1D allows users to process their NMR spectra within a GUI application and thus the macro-command sequence coming from this process can be saved.

• Outside NMRProcFlow Rnmr1D become an R package allowing users to replay the macro-command sequence generated within NMRProcFlow. Moreover, without using NMRProcFlow, this package can also be used to replace any 'home-made script' by a macro-command sequence.

• See the Macro-command Reference Guide to have more details about macro-commands.

Installation of some dependencies

• You may need to install a C++ compiler if not the case yet (see https://teuder.github.io/rcpp4everyone_en/020_install.html)

• Some R packages:

packages <- c("impute", "MassSpecWavelet","pcaMethods")
if (length(setdiff(packages, rownames(installed.packages()))) > 0) {
   if (paste(R.Version()$major,R.Version()$minor, sep=".") > "3.5") {
      if (!requireNamespace('BiocManager', quietly = TRUE))
          install.packages('BiocManager', repos='http://cran.rstudio.com/');
      BiocManager::install(setdiff(packages, rownames(installed.packages())), version = '3.8');
   } else {
      source('http://bioconductor.org/biocLite.R');
      biocLite(setdiff(packages, rownames(installed.packages())));
   }
}

packages <- c('doParallel', 'ptw', 'signal', 'speaq', 'base64enc', 'XML', 'igraph', 'ggplot2', 'plotly', 'plyr')
if (length(setdiff(packages, rownames(installed.packages()))) > 0) {
  install.packages(setdiff(packages, rownames(installed.packages())), repos='http://cran.rstudio.com')
}

Installation of the R package

• Note for Windows 7/10: Before performing the installation within R GUI it may require to specify the Compiler binaries path in the PATH environment variable so that the C++ code compilation will be correctly done ( check with Sys.getenv("PATH") )

require(devtools)
install_github("INRA/Rnmr1D", dependencies = TRUE)

Example of use

library(Rnmr1D)

# Test with the provided example data
data_dir <- system.file("extra", package = "Rnmr1D")
RAWDIR <- file.path(data_dir, "CD_BBI_16P02")
CMDFILE <- file.path(data_dir, "NP_macro_cmd.txt")
SAMPLEFILE <- file.path(data_dir, "Samples.txt")

# Detect the number of Cores
detectCores()

# Launch the pre-processing then the processing defined in the macro-command file
out <- Rnmr1D::doProcessing(RAWDIR, cmdfile=CMDFILE, samplefile=SAMPLEFILE, ncpu=detectCores())

# Have a look on returned data structure
ls(out)
ls(out$specMat)

### Stacked Plot with a perspective effect
dev.new()
plotSpecMat(out$specMat, ppm_lim=c(0.5,5), K=0.33)

### Overlaid Plot
dev.new()
plotSpecMat(out$specMat, ppm_lim=c(0.5,5), K=0, pY=0.1)

# Get the data matrix 
outMat <- getBucketsDataset(out, norm_meth='CSN')

# Get the Signal/Noise Ratio (SNR) matrix 
outSNR <- getSnrDataset(out, c(10.2,10.5), ratio=TRUE)

# Get the bucket table
outBucket <- getBucketsTable(out)

# Get the spectra data
spectra <- getSpectraData(out)

See a more complete illustation within the vignette

vignette("Rnmr1D")

You can access the vignette online : https://nmrprocflow.org/themes/html/Rnmr1D.html