spectral_matching: Spectral matching deprecated

View source: R/spectral-matching.R

spectral_matchingR Documentation

Spectral matching deprecated

Description

Perform spectral matching to spectral libraries using dot product cosine on a LC-MS/MS dataset and link to XCMS features.

msPurity::spectral_matching is deprecated - please use msPurity::spectralMatching for future use

Usage

spectral_matching(
  query_db_pth,
  ra_thres_l = 0,
  ra_thres_q = 2,
  cores = 1,
  pol = "positive",
  ppm_tol_prod = 10,
  ppm_tol_prec = 5,
  score_thres = 0.6,
  topn = NA,
  db_name = NA,
  library_db_pth = NA,
  instrument_types = NA,
  library_sources = "massbank",
  scan_ids = NA,
  pa = NA,
  xset = NA,
  grp_peaklist = NA,
  out_dir = ".",
  ra_w = 0.5,
  mz_w = 2,
  spectra_type_q = "scans",
  ra_thres_t = NA,
  target_db_pth = NA,
  rt_range = c(NA, NA),
  rttol = NA,
  match_alg = "dpc"
)

Arguments

query_db_pth

character; Path of the database of targets (queries) that will be searched against the library spectra. Generated either from frag4feature or from create_database functions.

ra_thres_l

numeric; Relative abundance threshold for library spectra

ra_thres_q

numeric; Relative abundance threshold for target (query) spectra (Peaks below this RA threshold will be excluded)

cores

numeric; Number of cores to use

pol

character; Polarity ['positive' or 'negative']

ppm_tol_prod

numeric; PPM tolerance to match to product

ppm_tol_prec

numeric; PPM tolerance to match to precursor

score_thres

numeric; Dot product cosine score threshold

topn

numeric [optional]; Only use top n matches

db_name

character [optional]; Name of the result database (e.g. can use CAMERA peaklist)

library_db_pth

character [optional]; path to library spectral SQLite database. Defaults to msPurityData package data.

instrument_types

vector [optional]; Vector of instrument types, defaults to all

library_sources

vector [optional]; Vector of library sources. Default option is for massbank only but the 'lipidblast' library is also available

scan_ids

vector [optional]; Vector of unique scan ids calculated from msPurity "pid". These scans will on used for the spectral matching. All scans will be used if set to NA

pa

purityA object [optional]; If target_db_pth set to NA, a new database can be created using pa, xset and grp_peaklist

xset

xcms object [optional]; If target_db_pth set to NA, a new database can be created using pa, xset and grp_peaklist

grp_peaklist

dataframe [optional]; If target_db_pth set to NA, a new database can be created using pa, xset and grp_peaklist

out_dir

character [optional]; If target_db_pth set to NA, Out directory for the SQLite result database

ra_w

numeric; Relative abundance weight for spectra

mz_w

numeric; mz weight for spectra

spectra_type_q

character; Type of fragmentation spectra from query to match with "scans" = all individual scans, "av_intra" = averaged spectra (intra), "av_inter" = averaged spectra (inter), "av_all" = averaged all spectra ignoring inter-intra relationships

ra_thres_t

numeric [deprecated]; The relative abundance threshold for the query spectra (use ra_thres_q for future use)

target_db_pth

character [deprecated]; The query database path (use query_db_pth for future use)

rt_range

vector [optional]; Vector of rention time range to filter the library spectra (rtmin, rtmax). Default is to ignore retention time range

rttol

numeric [optional]; Tolerance in time range between the Library and Query database retention time (in seconds) NA to ignore

match_alg

character; Can either use dot product cosine (dpc) or match factor (mf) for spectral matching. Defaults to dpc

Value

list of database details and dataframe summarising the results for the xcms features

Examples

#msmsPths <- list.files(system.file("extdata", "lcms", "mzML",
#                         package="msPurityData"), full.names = TRUE,
#                         pattern = "MSMS")
#xset <- xcms::xcmsSet(msmsPths)
#xset <- xcms::group(xset)
#xset <- xcms::retcor(xset)
#xset <- xcms::group(xset)

#pa  <- purityA(msmsPths)
#pa <- frag4feature(pa, xset)
#pa <- averageAllFragSpectra(pa)
#db_pth <- create_database(pa, xset)
#q_dbPth <- system.file("extdata", "tests", "db",
#                        "create_database_example.sqlite", package="msPurity")
#result <- spectral_matching(q_dbPth, spectra_type_q="av_all")

computational-metabolomics/msPurity documentation built on May 13, 2024, 7:36 p.m.