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,
...
)
Arguments
- resources
interactions not reported in these databases are removed. See
get_interaction_resources
for more information.- organism
Interactions are available for human, mouse and rat. Choose among: 9606 human (default), 10116 rat and 10090 Mouse
- 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.
- ...
Optional additional arguments.
Examples
grn <-
import_transcriptional_interactions(
resources = c('PAZAR', 'ORegAnno', 'DoRothEA')
)
#> Warning: The following resources are not available: PAZAR. Check the resource names for spelling mistakes.
grn
#> # A tibble: 25,339 × 16
#> source target sourc…¹ targe…² is_di…³ is_st…⁴ is_in…⁵ conse…⁶ conse…⁷ conse…⁸
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 P01106 O14746 MYC TERT 1 1 0 1 1 0
#> 2 P84022 P05412 SMAD3 JUN 1 1 0 1 1 0
#> 3 Q13485 P05412 SMAD4 JUN 1 1 0 1 1 0
#> 4 P08047 P04075 SP1 ALDOA 1 1 0 1 1 0
#> 5 P04637 P08069 TP53 IGF1R 1 0 1 1 0 1
#> 6 Q05516 P20248 ZBTB16 CCNA2 1 0 1 1 0 1
#> 7 Q01196 P08700 RUNX1 IL3 1 0 1 1 0 1
#> 8 P42224 P38936 STAT1 CDKN1A 1 1 0 1 1 0
#> 9 P40763 P38936 STAT3 CDKN1A 1 1 0 1 1 0
#> 10 Q04206 P08183 RELA ABCB1 1 1 0 1 1 0
#> # … with 25,329 more rows, 6 more variables: sources <chr>, references <chr>,
#> # curation_effort <dbl>, dorothea_level <chr>, n_references <dbl>,
#> # n_resources <int>, and abbreviated variable names ¹source_genesymbol,
#> # ²target_genesymbol, ³is_directed, ⁴is_stimulation, ⁵is_inhibition,
#> # ⁶consensus_direction, ⁷consensus_stimulation, ⁸consensus_inhibition