synapterPlgsAgreement.RdThis method checks the agreement between synapter analysis and PLGS results.
# S4 method for MSnSet synapterPlgsAgreement(object, …)
| object | An |
|---|---|
| … | further arguments, not used yet. |
MSnSet where the columns nIdentified,
nAgree, nDisagree and synapterPlgsAgreementRatio were
added to the feature data.
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).
See discussion on github: https://github.com/lgatto/synapter/issues/73
MSnSet documentation: MSnSet