Imports the enzyme-substrate (more exactly, enzyme-PTM) relationship database from https://omnipathdb.org/enzsub
Usage
import_omnipath_enzsub(
resources = NULL,
organism = 9606,
fields = NULL,
default_fields = TRUE,
references_by_resource = TRUE,
exclude = NULL,
...
)
Arguments
- resources
PTMs not reported in these databases are removed. See
get_ptms_databases
for more information.- 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
, toFALSE
.- default_fields
Whether to include the default fields (columns) for the query type. If
FALSE
, only the fields defined by the user in thefields
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.
- exclude
Character: datasets or resources to exclude.
- ...
Optional additional arguments.
Examples
enzsub <- import_omnipath_enzsub(
resources = c('PhosphoSite', 'SIGNOR'),
organism = 9606
)