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]