Convert an mzTab-M to MetaboLights MAF file using rmzTabM and metabolighteR

convertMzTab2MAF.R

library(rmzTabM)       ## https://lifs-tools.github.io/rmzTab-m/ 
library(metabolighteR) ## https://aberhrml.github.io/metabolighteR/

convertMzTab2MAF <- function(mzTabfile, MAFfile) {

  mzTabTable <- readMzTab(mzTabfile)

  ## To turn these tables into objects, use the R6 class constructor method `new()`:
  mzTabObject <- MzTab$new()$fromDataFrame(mzTabTable)
  metadata <- mzTabObject$metadata
  msassaynames <- sapply(metadata$assay, function(a) a$name)

  smlTable <- extractSmallMoleculeSummary(mzTabTable)
  smfTable <- extractSmallMoleculeFeatures(mzTabTable)
  #smeTable <- extractSmallMoleculeEvidence(mzTabTable)

  abundances <- as.matrix(smlTable[,which(grepl("abundance_assay", colnames(smlTable)))])
  colnames(abundances) <- msassaynames

  ##
  ## Writing as MAF file
  ##

  maf <- create.MAF(abundances=abundances)

  ## Adding in additional columns from MS-Dial output
  #maf[,""] <- smlTable[,""]

  maf[,"chemical_formula"] <- smlTable[,"chemical_formula"]
  maf[,"smiles"] <- smlTable[,"smiles"]
  maf[,"inchi"] <- smlTable[,"inchi"]
  maf[,"metabolite_identification"] <- smlTable[,"chemical_name"]

  ##
  ## This only works if sml and smf have same dim and same order !!!
  ##
  maf[,"retention_time"] <- smfTable[, "retention_time_in_seconds"]
  maf[,"mass_to_charge"] <- smfTable[, "exp_mass_to_charge"]

  ##
  ## Database handling in mzTab is more powerful than in MAF,
  ## multiple databases are allowed. This is NOT considered here

  maf[,"database"] <- metadata$database[[1]]$id ## https://github.com/lifs-tools/rmzTab-m/issues/24
  maf[,"database_version"] <- metadata$database[[1]]$version
  maf[,"database_identifier"] <- smlTable[,"database_identifier"] ## Mybe strip the mzTab PREFIX ?

  ## Would require normalisation/mapping between scoring systems:
  maf[,"reliability"] <- smlTable[,"best_id_confidence_value"]

  write.MAF(maf, MAFfile)
}

## Example invocation: 

## Reading the mzTab created by MS-Dial
## wget https://raw.githubusercontent.com/HUPO-PSI/mzTab/master/examples/2_0-Metabolomics_Release/msdial/lcmsms_dda_hydrophilic_height_mzTab.txt

## convertMzTab2MAF(mzTabfile="lcmsms_dda_hydrophilic_height_mzTab.txt", MAFfile="m_MTBLS007_v2_maf.tsv")