For a given filename (e.g. "test.mzML"), check the suffix and translate it to an PSI-MS CV term, e.g. 'MS:1000584'

The following mapping is currently known: .raw : MS:1000563 ! Thermo RAW format .mzML : MS:1000584 ! mzML format .mzData : MS:1000564 ! PSI mzData format .wiff : MS:1000562 ! ABI WIFF format .pkl : MS:1000565 ! Micromass PKL format .mzXML : MS:1000566 ! ISB mzXML format .yep : MS:1000567 ! Bruker/Agilent YEP format .dta : MS:1000613 ! Sequest DTA format .mzMLb : MS:1002838 ! mzMLb format

filenameToCV(filepath)

Arguments

filepath

A filename (with optional path)

Value

A CV term accession as string, e.g. 'MS:1000584'

Details

Falls back to 'MS:1000560 ! mass spectrometer file format' if no match could be found.

Upper/lowercase is ignored, i.e. "mzML == mzml".

Examples

  filenameToCV("test.mZmL")  # MS:1000584
#> [1] "MS:1000584"
  filenameToCV("test.raw")  # MS:1000563
#> [1] "MS:1000563"
  filenameToCV(c("test.raw", "bla.mzML"))
#>     test.raw     bla.mzML 
#> "MS:1000563" "MS:1000584"