support open file standards through Bioconductor mzR package - make it PSI friendly

[cpanse]

to benefit from to the fantastic PSI world.

[wolski]

Map columns from RawDiag to CV terms.

c("filename", "scanNumber", "StartTime", "BasePeakMass", "BasePeakIntensity", "TIC", "ScanType", "CycleNumber", "MSOrder", "MassAnalyzer", "PrecursorMass", "ChargeState", "IonInjectionTimems", "FTResolution", "MasterScanNumber", "LMCorrection", "ElapsedScanTimesec", "transient", "AGC", "AGCMode", "PrescanMode")

https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

[tobiasko]

I will most likely not manage to do this before 15th of May (application deadline).

[cpanse]

the code snippet below should do the job

#' mzR reader method
#'
#' @param object an mzR object
#'
#' @return an \code{\link{rawDiag}} object
#' @author Christian Panse <cp@fgcz.ethz.ch>, Witold E.Wolski <wew@fgcz.ethz.ch>
#' @example 
#' 
#' library(mzR)
#' mzmlFilename <- "PXD006932/Exp3A/20161213_NGHF_DBJ_SA_Exp3A_HeLa_1ug_15min_15000_01.mzML"
#' S <- as.rawDiag.mzR(openMSfile(mzmlFilename))
#' 
as.rawDiag.mzR <- function(object){
  #time.start <- Sys.time()
  runInfo <- runInfo(object)
  rv <- lapply(1:runInfo$scanCount, 
               function(x){data.frame(header(object, x))})
  rv <- bind_rows(rv)

  #time.end <- Sys.time()
  #message(time.start - time.end)

  rv <- rv[, c('acquisitionNum', 'retentionTime', 'basePeakMZ',
               'basePeakIntensity', 'totIonCurrent', 'msLevel', 'precursorMZ',
               'precursorCharge')]

  colnames(rv) <- c('scanNumber', 'StartTime', 'BasePeakMass',
                    'BasePeakIntensity', 'TIC', 'MSOrder', 'PrecursorMass',
                    'ChargeState')

  rv$filename <- basename(fileName(object))
  as.rawDiag(rv)
}