combineAnnotations: Combine Annotations

Description Usage Arguments Value Examples

View source: R/combineAnnotations.R

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 t.n.lawson@bham.ac.uk)

Usage

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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 t.n.lawson@bham.ac.uk). 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

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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)

msPurity documentation built on Jan. 14, 2021, 2:44 a.m.