combineAnnotations {msPurity} | R Documentation |
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.
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)
sm_resultPth |
character; |
metfrag_resultPth |
character; |
sirius_csi_resultPth |
character; |
probmetab_resultPth |
character; |
weights |
list; |
outPth |
character; |
silentRestErrors |
boolean; |
purityA object with slots for fragmentation-XCMS links
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'))