Find Consistent MS2 Fingerprints — find_consistent_ms2

Compare all MS2 fingerprints within the group to separate distinct groups based on MS2 profiles.

find_consistent_ms2_fingerprints(
  mz_set,
  MS2tol,
  cosine_cutoff = 0.95,
  create_plots = FALSE,
  rt_range = NULL
)

Arguments

mz_set: a set of peaks with a consistent parent mass m/z which may contain multiple species with distinct RT / MS2 fingerprints.
MS2tol: mass tolerance for grouping ms2 m/z values: see build_clamr_config.
cosine_cutoff: Minimum cosine similarity between a pair of MS2 fragment profiles to group them into a common cluster.
create_plots: TRUE/FALSE: should a summary plot be printed.
rt_range: optional if create_plots is FALSE, if create_plots is TRUE, length two numeric vector specifying the lower and upper limits of retention time for an experiment.

Value

assignments of parent peaks to distinct ms2 peak groups

Examples

MS2tol <- build_clamr_config(list(MS2tol = "20ppm"))$MS2tol
find_consistent_ms2_fingerprints(
  mz_set = clamr::mz_set_example,
  MS2tol = MS2tol, create_plots = TRUE, rt_range = c(0, 22)
)
#> Warning: `select_()` was deprecated in dplyr 0.7.0.
#> Please use `select()` instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
#> Error in loadNamespace(x): there is no package called ‘fastcluster’