Pbase parametrisation infrastructure.
Pbase parameters can be generated with the
Pparams instances control various aspects of
Pbase functions, as described in the Slots section
below. If no parameters are passed to the respective functions,
default values from
Pparams() are used.
The format of the protein sequence fasta
database used to generate the
Proteins object. Currently
"UniProt" is supported.
"RefSeq" will be added
as well as a mechanism to support arbitrary and custom fasta
The format of the identification data files
used to add
mzIdentML is supported.
Package to be used to load the
identification data. Currently one of
mzR (via the
psms functions) or
flatten functions). Differences between
these two architectures include the metadata available in the
pfeatures, speed and stability (
is much faster but less mature and currently susceptible to
logical defining if the various
functions display messages (default) or remain silent.
signature(object = "Pparams"): ...
Laurent Gatto <[email protected]>
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