## S3 method for class 'mzIDCollection':
show(object)## S3 method for class 'mzIDCollection':
length(x)
as.list.mzIDCollection(object)
## S3 method for class 'mzIDCollection':
removeDecoy(object)
## S3 method for class 'mzIDCollection':
names(x)
## S3 method for class 'mzIDCollection,character':
names(x) <- value
## S3 method for class 'mzIDCollection,numeric,missing':
[[(x, i, j, ...)
## S3 method for class 'mzIDCollection,character,missing':
[[(x, i, j, ...)
## S3 method for class 'mzIDCollection,numeric,missing,missing':
[(x, i, j, drop)
## S3 method for class 'mzIDCollection,character,missing,missing':
[(x, i, j, drop)
## S3 method for class 'mzIDCollection,logical,missing,missing':
[(x, i, j, drop)
## S3 method for class 'mzIDCollection':
c(x, y, ..., recursive = FALSE)
## S3 method for class 'mzIDCollection':
database(object, safeNames = TRUE)
## S3 method for class 'mzIDCollection':
evidence(object, safeNames = TRUE)
## S3 method for class 'mzIDCollection':
parameters(object)
## S3 method for class 'mzIDCollection':
software(object)
## S3 method for class 'mzIDCollection':
files(object)
## S3 method for class 'mzIDCollection':
peptides(object, safeNames = TRUE)
## S3 method for class 'mzIDCollection':
modifications(object)
## S3 method for class 'mzIDCollection':
id(object, safeNames = TRUE)
## S3 method for class 'mzIDCollection':
scans(object, safeNames = TRUE)
## S3 method for class 'mzIDCollection':
idScanMap(object)
show
: A short summary of the content of the objectlength
: Return the number of mzID object in the collectionremoveDecoy
: Removes decoys in all mzID object in collectionnames
: Get the names of the mzID object stored in the
collectionnames<-
: Set the names of the mzID object stored in the
collection[[
: Extract an mzID object by index[[
: Extract an mzID object by name[
: Subset collection by index[
: Subset collection by name[
: Subset collection by logical valuec
: Combine mzIDCollction and mzID objectsdatabase
: Get the database used for searchingevidence
: Get the evidence from the peptide searchparameters
: Get the parameters used for the searchsoftware
: Get the software used to arrive at the resultsfiles
: Get the data files used for the analysispeptides
: Get the peptides identified.modifications
: Get the modification on the identified peptidesid
: Get the identification resultsscans
: Get the scans matched to peptidesidScanMap
: Get the link between scans and identificationsmzID
mzIDCollection
Other mzID.classes: mzID-class
,
mzIDdatabase-class
,
mzIDevidence-class
,
mzIDparameters-class
,
mzIDpeptides-class
,
mzIDpsm-class