combineAnnotations: Combine Annotations

In computational-metabolomics/msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

Combine Annotations

Description

Combine the annotation results from msPurity spectral matching, MetFrag, Sirius CSI:FingerID, probmetab and any generic MS1 lookup software (e.g. results from the BEAMS software)

The annotation results are then aligned by inchikey and XCMS grouped feature.

The tool has to be run with a local compound database (available on request - contact [e-mail])

Usage

combineAnnotations(
  sm_resultPth,
  compoundDbPth,
  metfrag_resultPth = NA,
  sirius_csi_resultPth = NA,
  probmetab_resultPth = NA,
  ms1_lookup_resultPth = NA,
  ms1_lookup_dbSource = "hmdb",
  ms1_lookup_checkAdducts = FALSE,
  ms1_lookup_keepAdducts = c("[M+H]+", "[M-H]-"),
  weights = list(sm = 0.3, metfrag = 0.2, sirius_csifingerid = 0.2, probmetab = 0,
    ms1_lookup = 0.05, biosim = 0.25),
  compoundDbType = "sqlite",
  compoundDbName = NA,
  compoundDbHost = NA,
  compoundDbPort = NA,
  compoundDbUser = NA,
  compoundDbPass = NA,
  outPth = NA,
  summaryOutput = TRUE
)

Arguments

sm_resultPth	character; Path to the msPurity SQLite database used for spectral matching
compoundDbPth	character; Path to local compound database with pubchem, hmdb, KEGG and metab_compound summary table (full database available on request - contact [e-mail]). This is only applicable if using "compoundDbType sqlite")
metfrag_resultPth	character; Path to the tsv table of metfrag results
sirius_csi_resultPth	character; Path to the tsv table of Sirius CSI:Finger ID results
probmetab_resultPth	character; Path to the tsv table of Probmetab results
ms1_lookup_resultPth	character; Path to generic tsv table of MS1 lookup results
ms1_lookup_dbSource	character; Source of the compound database used for ms1_lookup (currently only supports HMDB, KEGG or PubChem)
ms1_lookup_checkAdducts	boolean; Check if adducts match to those found in CAMERA (requires the database to have been created with CAMERA object)
ms1_lookup_keepAdducts	vecotr; Keep only adducts found from the MS1 lookup that are found in this vector
weights	list;
compoundDbType	character; Database type for compound database can be either (sqlite, postgres or mysql)
compoundDbName	character; Database name (only applicable for postgres and mysql)
compoundDbHost	character; Database host (only applicable for postgres and mysql)
compoundDbPort	character; Database port (only applicable for postgres and mysql)
compoundDbUser	character; Database user (only applicable for postgres and mysql)
compoundDbPass	character; Database pass (only applicable for postgres and mysql) - Note this is not secure!
outPth	character;
summaryOutput	boolean; If a summary dataframe is to be created

Value

purityA object with slots for fragmentation-XCMS links

Examples

metfrag_resultPth <- system.file("extdata", "tests", "external_annotations",
                                      "metfrag.tsv", package="msPurity")
# run the standard spectral matching workflow to get the sm_resultPth
sm_resultPth <- system.file("extdata","tests", "sm",
                        "spectralMatching_result.sqlite", package="msPurity")
compoundDbPth <- system.file("extdata", "tests", "db",
                          "metab_compound_subset.sqlite", package="msPurity")
combined <- combineAnnotations(sm_resultPth,
                             metfrag_resultPth,
                             outPth=file.path(tempdir(), 'combined.sqlite'),
                             compoundDbPth=compoundDbPth)

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