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Annotate spectra

Source: R/annotate_spectra.R
annotate_spectra.Rd

This function annotates spectra

Usage

annotate_spectra(
  input = get_params(step = "annotate_spectra")$files$spectral$raw,
  library = get_params(step = "annotate_spectra")$files$libraries$spectral,
  polarity = get_params(step = "annotate_spectra")$ms$polarity,
  output = get_params(step = "annotate_spectra")$files$annotations$raw$spectral$spectral,
  threshold = get_params(step =
    "annotate_spectra")$annotations$thresholds$ms2$similarity$annotation,
  ppm = get_params(step = "annotate_spectra")$ms$tolerances$mass$ppm$ms2,
  dalton = get_params(step = "annotate_spectra")$ms$tolerances$mass$dalton$ms2,
  qutoff = get_params(step = "annotate_spectra")$ms$thresholds$ms2$intensity,
  approx = get_params(step = "annotate_spectra")$annotations$ms2approx
)

Arguments

input

Query file containing spectra. Currently an '.mgf' file

library

Library containing spectra to match against. Can be '.mgf' or '.sqlite' (Spectra formatted)

polarity

MS polarity. Must be 'pos' or 'neg'.

output

Output file.

threshold

Minimal similarity to report

ppm

Relative ppm tolerance to be used

dalton

Absolute Dalton tolerance to be used

qutoff

Intensity under which ms2 fragments will be removed.

approx

Perform matching without precursor match

Details

It takes two files as input. A query file that will be matched against a library file.

Examples

if (FALSE) { # \dontrun{
tima:::copy_backbone()
go_to_cache()
get_file(
  url = get_default_paths()$urls$examples$spectra_mini,
  export = get_params(step = "annotate_spectra")$files$spectral$raw
)
get_file(
  url = get_default_paths()$urls$examples$spectral_lib_mini$with_rt,
  export = get_default_paths()$data$source$libraries$spectra$exp$with_rt
)
annotate_spectra(
  library = get_default_paths()$data$source$libraries$spectra$exp$with_rt
)
unlink("data", recursive = TRUE)
} # }