spectral_matching {msPurity} | R Documentation |
Perform spectral matching to spectral libraries using dot product cosine on a LC-MS/MS dataset and link to XCMS features.
spectral_matching(target_db_pth, ra_thres_l = 0, ra_thres_t = 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 = ".")
target_db_pth |
character; Path of the database of targets 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_t |
numeric; Relative abundance threshold for target 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 [deprecated]; If target_db_pth set to NA, a new database can be created using pa, xset and grp_peaklist |
xset |
xcms object [deprecated]; If target_db_pth set to NA, a new database can be created using pa, xset and grp_peaklist |
grp_peaklist |
dataframe [deprecated]; If target_db_pth set to NA, a new database can be created using pa, xset and grp_peaklist |
out_dir |
character [deprecated]; If target_db_pth set to NA, Out directory for the SQLite result database |
list of database details and dataframe summarising the results for the xcms features
msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS") xset <- xcms::xcmsSet(msmsPths, nSlaves = 1) xset <- xcms::group(xset) xset <- xcms::retcor(xset) xset <- xcms::group(xset) pa <- purityA(msmsPths) pa <- frag4feature(pa, xset, create_db=TRUE) #NOTE that scan_ids here are refer the unique scan id calculated by purityA (pids). #Only required if you want to limit the spectral matching to certain scans result <- spectral_matching(pa@db_path, scan_ids = c(1120, 366, 1190, 601, 404,1281, 1323, 1289))