Description Usage Arguments Value Examples
View source: R/spectral-matching.R
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | 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"
)
|
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 |
list of database details and dataframe summarising the results for the xcms features
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | #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")
|
Loading required package: Rcpp
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.