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Extract features from measurement files with an algorithm

scanBatch.Rd

The spectral library is used to scan mzXML measurment files for compounds using the DBAS algorithm. The parameters for DBAS and file locations (measurement files and spectral library) are stored the `dbasMsrawfilesBatch` object.

The mzXML measurment files are scanned for all features using the NTS algorithm. The spectral library is used to annotated known features. The parameters for NTS and file locations (measurement files and spectral library) are stored in are stored the `ntsMsrawfilesBatch` object.

Usage 

scanBatch(msrawfilesBatch, ...)

# S3 method for class 'dbasMsrawfilesBatch'
scanBatch(msrawfilesBatch, compsToProcess = NULL, showProgress = FALSE)

# S3 method for class 'ntsMsrawfilesBatch'
scanBatch(msrawfilesRecords, forNtsworkflow = FALSE)

Arguments

msrawfilesBatch

object inheriting `msrawfilesBatch` (`list` of `msrawfilesRecord`s)

compsToProcess

Character vector of compounds names to include in the scanning (default is all compounds in the spectral library)

showProgress

Logical, show progress bar? (for interacte use, default false)

forNtsworkflow

logical, should the results be prepared for the ntsworkflow non-target app?

Value

a `dbasResult` (`list` of 7 tables) including `peakList`, `reintegrationResults` etc.

an `ntsResult` object with the tables `peakList`, `sampleList`, `alignmentTable`, `annotationTable`

Examples 

if (FALSE) { # \dontrun{
dbComm <- getDbComm()
recs <- getTableAsRecords(
  dbComm, 
  "ntsp25.2_msrawfiles", 
  searchBlock = list(query = list(regexp = list(filename = "Des_19_.._pos.mzXML"))),
  newDbasMsrawfilesRecord
)
recsBlanks <- getTableAsRecords(
  dbComm, 
  "ntsp25.2_msrawfiles", 
  searchBlock = list(query = list(regexp = list(path = ".*mud_pos/BW.*"))), 
  newDbasMsrawfilesRecord
)
newBatch <- newDbasMsrawfilesBatch(c(recs, recsBlanks))
res <- scanBatch(newBatch, "Methyltriphenylphosphonium")
} # }