import_all_interactions | R Documentation |
The interaction datasets currently available in OmniPath:
import_all_interactions(
resources = NULL,
organism = 9606,
dorothea_levels = c("A", "B"),
exclude = NULL,
fields = NULL,
default_fields = TRUE,
references_by_resource = TRUE,
strict_evidences = FALSE,
types = NULL,
...
)
import_AllInteractions(...)
resources |
interactions not reported in these databases are
removed. See |
organism |
Interactions are available for human, mouse and rat. Choose among: 9606 human (default), 10116 rat and 10090 Mouse |
dorothea_levels |
The confidence levels of the dorothea interactions (TF-target) which range from A to D. Set to A and B by default. |
exclude |
Character: datasets or resources to exclude. |
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. |
strict_evidences |
Logical: restrict the evidences to the queried datasets and resources. If set to FALSE, the directions and effect signs and references might be based on other datasets and resources. |
types |
Character: interaction types, such as "transcriptional", "post_transcriptional", "post_translational", etc. |
... |
Passed to |
omnipath: the OmniPath data as defined in the paper, an arbitrary optimum between coverage and quality pathwayextra: activity flow interactions without literature reference kinaseextra: enzyme-substrate interactions without literature reference ligrecextra: ligand-receptor interactions without literature reference dorothea: transcription factor (TF)-target interactions from DoRothEA tf_target: transcription factor (TF)-target interactions from other resources mirnatarget: miRNA-mRNA interactions tf_mirna: TF-miRNA interactions lncrna_mrna: lncRNA-mRNA interactions
A dataframe containing all the datasets in the interactions query
get_interaction_resources
interaction_graph
print_interactions
interactions <- import_all_interactions(
resources = c('HPRD', 'BioGRID'),
organism = 9606
)
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