combineAnnotations {msPurity}R Documentation

Combine Annotations

Description

Combine the annotation results from msPurity spectral matching, MetFrag, Sirius CSI:FingerID and probmetab based on weighted scores for each technique aligning each annotation by inchikey and XCMS grouped feature.

Usage

combineAnnotations(sm_resultPth, metfrag_resultPth = NA,
  sirius_csi_resultPth = NA, probmetab_resultPth = NA,
  weights = list(sm = 0.4, metfrag = 0.25, sirius_csifingerid = 0.25,
  probmetab = 0.1), outPth = NA, silentRestErrors = FALSE)

Arguments

sm_resultPth

character;

metfrag_resultPth

character;

sirius_csi_resultPth

character;

probmetab_resultPth

character;

weights

list;

outPth

character;

silentRestErrors

boolean;

Value

purityA object with slots for fragmentation-XCMS links

Examples

metfrag_resultPth <- system.file("extdata", "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")

combined <- combineAnnotations(sm_resultPth, metfrag_resultPth, outPth=file.path(tempdir(), 'combined.sqlite'))

[Package msPurity version 1.10.0 Index]