dorothea | R Documentation |
Imports the dataset from: https://omnipathdb.org/interactions?datasets=dorothea which contains transcription factor (TF)-target interactions from DoRothEA https://github.com/saezlab/DoRothEA DoRothEA is a comprehensive resource of transcriptional regulation, consisting of 16 original resources, in silico TFBS prediction, gene expression signatures and ChIP-Seq binding site analysis.
dorothea(
resources = NULL,
organism = 9606,
dorothea_levels = c("A", "B"),
fields = NULL,
default_fields = TRUE,
references_by_resource = TRUE,
exclude = NULL,
strict_evidences = TRUE,
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. For other organisms, the data will be translated by orthologous gene pairs from human. In this case, only one organism can be provided. |
dorothea_levels |
Vector detailing the confidence levels of the
interactions to be downloaded. In dorothea, every TF-target interaction
has a confidence score ranging from A to E, being A the most reliable
interactions.
By default we take A and B level interactions ( |
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. In case of DoRothEA this is not desirable for most of the applications. For most of the other interaction querying functions it is 'FALSE' by default. |
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 of TF-target interactions from DoRothEA
collectri
import_transcriptional_interactions
import_tf_target_interactions
get_interaction_resources
import_all_interactions
interaction_graph
print_interactions
dorothea_grn <- dorothea(
resources = c('DoRothEA', 'ARACNe-GTEx_DoRothEA'),
organism = 9606,
dorothea_levels = c('A', 'B', 'C')
)
dorothea_grn
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