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TF-target interactions from DoRothEA

Source: R/interactions.R
dorothea.Rd

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.

Usage

dorothea(
  resources = NULL,
  organism = 9606,
  dorothea_levels = c("A", "B"),
  fields = NULL,
  default_fields = TRUE,
  references_by_resource = TRUE,
  exclude = NULL,
  strict_evidences = TRUE,
  ...
)

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.

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.

...

optional additional arguments

Value

A dataframe of TF-target interactions from DoRothEA

See also

Examples

dorothea_grn <- dorothea(
    resources = c('DoRothEA', 'ARACNe-GTEx_DoRothEA'),
    organism = 9606,
    dorothea_levels = c('A', 'B', 'C')
)
dorothea_grn
#> # A tibble: 32,617 × 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>     <int>   <int>   <int>   <int>   <int>   <int>
#>  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 32,607 more rows, 6 more variables: sources <chr>, references <chr>,
#> #   curation_effort <int>, dorothea_level <chr>, n_references <int>,
#> #   n_resources <int>, and abbreviated variable names ¹​source_genesymbol,
#> #   ²​target_genesymbol, ³​is_directed, ⁴​is_stimulation, ⁵​is_inhibition,
#> #   ⁶​consensus_direction, ⁷​consensus_stimulation, ⁸​consensus_inhibition