annotate_spectra: Annotate spectra

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

Annotate spectra

Description

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

## Not run: 
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)

## End(Not run)

taxonomicallyinformedannotation/tima-r documentation built on Dec. 20, 2024, 9:32 a.m.