import_mirnatarget_interactions | R Documentation |
Imports the dataset from: https://omnipathdb.org/interactions?datasets=mirnatarget, which contains miRNA-mRNA interactions.
import_mirnatarget_interactions(
resources = NULL,
organism = 9606,
fields = NULL,
default_fields = TRUE,
references_by_resource = TRUE,
exclude = NULL,
strict_evidences = FALSE,
genesymbol_resource = NULL,
...
)
resources |
interactions not reported in these databases are
removed. See |
organism |
Character or integer: Name or NCBI Taxonomy ID of one or organisms. The web service currently provides interactions for human, mouse and rat. |
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. |
exclude |
Character: datasets or resources to exclude. |
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. |
genesymbol_resource |
Character: either "uniprot" or "ensembl". The former leaves intact the gene symbols returned by the web service, originally set from UniProt. The latter updates the gene symbols from Ensembl, which uses a slightly different gene symbol standard. In this case a few records will be duplicated, where Ensembl provides ambiguous translation. |
... |
optional additional arguments |
A dataframe containing miRNA-mRNA interactions
get_interaction_resources
import_all_interactions
interaction_graph
print_interactions
interactions <-
import_mirnatarget_interactions(
resources = c('miRTarBase', 'miRecords')
)
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