cfm_search: Spectral similarity searching against a pre-computed CFM...

In gjgetzinger/cfmR: R Wrapper for calling the Competitive Fragmentation Modeling for Metabolite Identifiction (CFM-ID) algorithm

Description

Spectral similarity searching against a pre-computed CFM library

Usage

cfm_search(
  query_spectrum,
  exact_mass = NULL,
  mol_form = NULL,
  db_file = NULL,
  spec_table_name = NULL,
  mol_table_name = NULL,
  molprop_table_name = NULL,
  ID = NULL,
  fun = c("common", "cor", "dotproduct"),
  bin = 1,
  pol = c("negative", "positive"),
  ppm = 10,
  excl_precur = F
)

Arguments

query_spectrum	An MSnbase::Spectrum2 object to search against the library
exact_mass	The neutral exact mass of the query spectrum
mol_form	The molecular formula assigned to the query spectrum.
db_file	A database file containing the CFM precomputed spectra
spec_table_name	The name of the table containing the precomputed spectra
mol_table_name	The name of the table containing molecules
molprop_table_name	The name of the table continaing molecular properties
ID	Values to filter by. Corresponds to the ID column in the table. If NULL than all spectra from the library are compared.
fun	Function to use for spectral comparrison (common, cor, or dotproduct). See MSnbase::compareSpectra.
bin	Bin size for peak patching. See MSnbase::compareSpectra for details.
pol	Polarity (positive or negative)
ppm	Mass error for filtering molecules by neutral mass
excl_precur	Should precursor ion from query spectrum be excluded. (T/F)

Value

A tibble with variables ID,

gjgetzinger/cfmR documentation built on May 11, 2020, 1 p.m.