dist_ms2 calculates and stores all non-zero distance values above
the user defined cutoff (default = 0.3).
Usage
dist_ms2(
data,
cutoff,
precursor_threshold,
score_params,
min_peaks = 6,
number_of_threads = 1
)Arguments
- data
the object generated from
ms2_ms1_compare().- cutoff
The maximum distance value (
numeric) to store a pairwise comparison. The default of .3 corresponds to a cosine score of .7, meaning pairs with a score of .7 or higher will be stored in the matrix.- precursor_threshold
Precursor mz tolerance. MS2 scans with a difference in precursor mz less than or equal to this value will be scored. Disable this by setting this value to -1 or less.
- score_params
Parameters for scoring method to be applied. See
modified_cosine_params()andspec_entropy_params()for more details.- min_peaks
the minimum number of peaks that need to be present before you compare the ms2 spectra.
- number_of_threads
the number of threads you wish to use for this calculation.
Details
This function takes a mass_data object as input and calculates distance
between ms2 peaks. Currently, MS1 features without MS2 peaks returns
no distance value. Distance can be calculated with method "gnps"
or "spectral_entropy". A sparse matrix is returned.
Examples
data <-
import_all_data(peak_table =
mums2::mums2_example("botryllus_pt_small.csv"),
metadata =
mums2::mums2_example("boryillus_metadata.csv"),
format = "None")
matched_data <- ms2_ms1_compare(mums2_example("botryllus_v2.gnps.mgf"),
data, 1, 6)
#> Reading: /home/runner/work/_temp/Library/mums2/extdata/botryllus_v2.gnps.mgf ...
#> 17/349 peaks have an MS2 spectra.
dist_gnps <- dist_ms2(data = matched_data,
cutoff = 0.3, precursor_threshold = 2,
score_params = modified_cosine_params(0.5), min_peaks = 0,
number_of_threads = 2)
dist_entropy <- dist_ms2(data = matched_data,
cutoff = 0.3, precursor_threshold = 2,
score_params = spec_entropy_params(), min_peaks = 0,
number_of_threads = 2)