synapterPlgsAgreement,MSnSet-method {synapter} | R Documentation

## Synapter/PLGS Agreement

### Description

This method checks the agreement between synapter analysis and PLGS results.

### Usage

    ## S4 method for signature 'MSnSet'
    synapterPlgsAgreement(object, ...)

### Arguments

`object` | An `MSnSet` object.
`...` | further arguments, not used yet.

### Details

Each synapter object has `synapterPlgsAgreement` column in its `MatchedEMRTs` `data.frame` (see `writeMatchedEMRTs`). After converting the synapter object into an `MSnSet` instance via `as(synapterobject, "MSnSet"` this column could be find in the feature data (`fData(msnset)$synapterPlgsAgreement`).
In the `synapterPlgsAgreement` each peptide is classified as:

- `"agree"`: EMRT identified in identification and quantitation run by PLGS and same EMRT matched in synapter's grid search.

- `"disagree"`: EMRT identified in identification and quantitation run by PLGS and a different EMRT was matched in synapter's grid search.

- `"no_plgs_id"`: EMRT was not identified in the quantitation run by PLGS but matched in synapter's grid search.

- `"no_synapter_transfer"`: EMRT was identified in the identification and quantitation run by PLGS but not matched in synapter's grid search.

- `"no_id_or_transfer"`: EMRT was not identified in the quantitation run by PLGS and not matched in synapter's grid search.

- `"multiple_ident_matches"`: a single quantitation EMRT was matched by synapter to multiple identification EMRTs found by PLGS (could happen if the grid search parameters are too relaxed).

After combining multiple `MSnSet` the method `synapterPlgsAgreement` adds additional columns to the feature data:

- `nIdentified`: how often a peptide was identified across multiple runs?

- `nAgree`: how often a peptide was identified by PLGS and synapter across multiple runs (counts `"agree"` entries)?

- `nDisagree`: how often a peptide was differently identified by PLGS and synapter across multiple runs (counts `"disagree"` entries)?

- `synapterPlgsAgreementRatio`: `nAgree/(nAgree + nDisagree)`.

### Value

`MSnSet` where the columns `nIdentified`, `nAgree`, `nDisagree` and `synapterPlgsAgreementRatio` were added to the feature data.

### Author(s)

Sebastian Gibb mail@sebastiangibb.de

### References

See discussion on github: https://github.com/lgatto/synapter/issues/73

### See Also

MSnSet documentation: `MSnSet`

[Package synapter version 2.4.1 Index]