import_omnipath_enzsub {OmnipathR} | R Documentation |
Imports the enzyme-substrate (more exactly, enzyme-PTM) relationship database from https://omnipathdb.org/enzsub
import_omnipath_enzsub( resources = NULL, organism = 9606, fields = NULL, default_fields = TRUE, references_by_resource = TRUE, exclude = NULL, ... )
resources |
PTMs not reported in these databases are
removed. See |
organism |
PTMs are available for human, mouse and rat. Choose among: 9606 human (default), 10116 rat and 10090 Mouse |
fields |
You can define here additional fields to be added to the
result. If used, set the next argument, |
default_fields |
Whether to include the default fields (columns) for
the query type. If |
references_by_resource |
if FALSE, removes the resource name prefixes from the references (PubMed IDs); this way the information which reference comes from which resource will be lost and the PubMed IDs will be unique. |
exclude |
Character: datasets or resources to exclude. |
... |
Optional additional arguments. |
A data frame containing the information about ptms
enzsub <- import_omnipath_enzsub( resources = c('PhosphoSite', 'SIGNOR'), organism = 9606 )