import_omnipath_enzsub {OmnipathR} | R Documentation |
Imports the enzyme-substrate (more exactly, enzyme-PTM) relationship database from https://omnipathdb.org/enzsub
import_omnipath_enzsub( cache_file = NULL, resources = NULL, organism = 9606, fields = NULL, default_fields = TRUE, references_by_resource = TRUE, ... ) import_Omnipath_PTMS(...) import_OmniPath_PTMS(...)
cache_file |
path to an earlier data file |
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 |
The user can define here the fields to be added. If used, set the next argument, 'default_fields', to FALSE. |
default_fields |
whether to include the default fields (columns) for the query type. If FALSE, only the fields defined by the user in the 'fields' argument will be added. |
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. |
... |
Passed to |
A data frame containing the information about ptms
get_ptms_databases,
import_omnipath_interactions
ptms = import_omnipath_enzsub( resources = c('PhosphoSite', 'SIGNOR'), organism = 9606 )