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(dorothea_levels = c("A", "B"), ...)Arguments
- 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.- ...
Arguments passed on to
omnipath_queryorganismCharacter or integer: name or NCBI Taxonomy ID of the organism. OmniPath is built of human data, and the web service provides orthology translated interactions and enzyme-substrate relationships for mouse and rat. For other organisms and query types, orthology translation will be called automatically on the downloaded human data before returning the result.
resourcesCharacter vector: name of one or more resources. Restrict the data to these resources. For a complete list of available resources, call the `get_<query_type>_resources` functions for the query type of interst.
genesymbolsCharacter or logical: TRUE or FALS or "yes" or "no". Include the `genesymbols` column in the results. OmniPath uses UniProt IDs as the primary identifiers, gene symbols are optional.
fieldsCharacter vector: additional fields to include in the result. For a list of available fields, call `query_info("interactions")`.
default_fieldsLogical: if TRUE, the default fields will be included.
silentLogical: if TRUE, no messages will be printed. By default a summary message is printed upon successful download.
logicalsCharacter vector: fields to be cast to logical.
formatCharacter: if "json", JSON will be retrieved and processed into a nested list; any other value will return data frame.
download_argsList: parameters to pass to the download function, which is `readr::read_tsv` by default, and `jsonlite::safe_load`.
references_by_resourceLogical: if TRUE,, in the `references` column the PubMed IDs will be prefixed with the names of the resources they are coming from. If FALSE, the `references` column will be a list of unique PubMed IDs.
add_countsLogical: if TRUE, the number of references and number of resources for each record will be added to the result.
licenseCharacter: license restrictions. By default, data from resources allowing "academic" use is returned by OmniPath. If you use the data for work in a company, you can provide "commercial" or "for-profit", which will restrict the data to those records which are supported by resources that allow for-profit use.
passwordCharacter: password for the OmniPath web service. You can provide a special password here which enables the use of `license = "ignore"` option, completely bypassing the license filter.
excludeCharacter vector: resource or dataset names to be excluded. The data will be filtered after download to remove records of the excluded datasets and resources.
json_paramList: parameters to pass to the `jsonlite::fromJSON` when processing JSON columns embedded in the downloaded data. Such columns are "extra_attrs" and "evidences". These are optional columns which provide a lot of extra details about interactions.
strict_evidencesLogical: reconstruct the "sources" and "references" columns of interaction data frames based on the "evidences" column, strictly filtering them to the queried datasets and resources. Without this, the "sources" and "references" fields for each record might contain information for datasets and resources other than the queried ones, because the downloaded records are a result of a simple filtering of an already integrated data frame.
genesymbol_resourceCharacter: "uniprot" (default) or "ensembl". The OmniPath web service uses the primary gene symbols as provided by UniProt. By passing "ensembl" here, the UniProt gene symbols will be replaced by the ones used in Ensembl. This translation results in a loss of a few records, and multiplication of another few records due to ambiguous translation.
cacheLogical: use caching, load data from and save to the. The cache directory by default belongs to the user, located in the user's default cache directory, and named "OmnipathR". Find out about it by
omnipath_get_cachedir. Can be changed byomnipath_set_cachedir.
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 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 P08047 P04075 SP1 ALDOA 1 1
#> 5 P04637 P08069 TP53 IGF1R 1 0
#> 6 Q05516 P20248 ZBTB16 CCNA2 1 0
#> 7 Q01196 P08700 RUNX1 IL3 1 0
#> 8 P42224 P38936 STAT1 CDKN1A 1 1
#> 9 P40763 P38936 STAT3 CDKN1A 1 1
#> 10 Q04206 P08183 RELA ABCB1 1 1
#> # ℹ 32,607 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>