Imports all TF-target interactions from OmniPath
Source:R/interactions.R
import_transcriptional_interactions.Rd
Imports the dataset from: https://omnipathdb.org/interactions?datasets=tf_target,dorothea, which contains transcription factor-target protein coding gene interactions.
Usage
import_transcriptional_interactions(
resources = NULL,
organism = 9606,
dorothea_levels = c("A", "B"),
references_by_resource = TRUE,
exclude = NULL,
strict_evidences = FALSE,
genesymbol_resource = NULL,
...
)
Arguments
- resources
interactions not reported in these databases are removed. See
get_interaction_resources
for more information.- 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 (
c(A, B)
). It is to note that E interactions are not available in OmnipathR.- 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.
Examples
grn <-
import_transcriptional_interactions(
resources = c('PAZAR', 'ORegAnno', 'DoRothEA')
)
#> NULL
#> Warning: The following resources are not available: PAZAR. Check the resource names for spelling mistakes.
grn
#> # A tibble: 31,896 × 16
#> source target source_genesymbol target_genesymbol is_directed is_stimulation
#> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 P01106 O14746 MYC TERT 1 1
#> 2 P84022 P05412 SMAD3 JUN 1 1
#> 3 Q13485 P05412 SMAD4 JUN 1 1
#> 4 Q04206 P25445 RELA FAS 1 1
#> 5 P08047 P04075 SP1 ALDOA 1 1
#> 6 P04637 P08069 TP53 IGF1R 1 0
#> 7 Q05516 P20248 ZBTB16 CCNA2 1 0
#> 8 Q01196 P08700 RUNX1 IL3 1 0
#> 9 P42224 P38936 STAT1 CDKN1A 1 1
#> 10 P40763 P38936 STAT3 CDKN1A 1 1
#> # ℹ 31,886 more rows
#> # ℹ 10 more variables: is_inhibition <dbl>, consensus_direction <dbl>,
#> # consensus_stimulation <dbl>, consensus_inhibition <dbl>, sources <chr>,
#> # references <chr>, curation_effort <dbl>, dorothea_level <chr>,
#> # n_references <dbl>, n_resources <int>