library("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(
libraries = get_default_paths()$data$source$libraries$spectra$exp$with_rt
)
unlink("data", recursive = TRUE)Annotate spectra
Description
This function annotates spectra
Usage
annotate_spectra(
input = get_params(step = "annotate_spectra")\$files\$spectral\$raw,
libraries = 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,
method = get_params(step = "annotate_spectra")\$similarities\$methods\$annotations,
threshold = get_params(step = "annotate_spectra")\$similarities\$thresholds\$annotations,
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 |
libraries
|
Libraries containing spectra to match against. Can be ‘.mgf’ or ‘.sqlite’ (Spectra formatted) |
polarity
|
MS polarity. Must be ‘pos’ or ‘neg’. |
output
|
Output file. |
method
|
Similarity method |
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.