Retrieve a static table from OmniPathSource:
A few resources and datasets are available also as plain TSV files and can be accessed without TLS. The purpose of these tables is to make the most often used OmniPath data available on computers with configuration issues. These tables are not the recommended way to access OmniPath data, and a warning is issued each time they are accessed.
static_table( query, resource, organism = 9606L, strict_evidences = TRUE, wide = TRUE, dorothea_levels = c("A", "B", "C") )
Character: a query type such as "annotations" or "interactions".
Character: name of the resource or dataset, such as "CollecTRI" or "PROGENy".
Integer: NCBI Taxonomy of the organism: 9606 for human, 10090 for mouse and 10116 for rat.
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.
Convert the annotation table to wide format, which corresponds more or less to the original resource. If the data comes from more than one resource a list of wide tables will be returned. See examples at
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 here we take A, B and C level interactions (
c("A", "B", "C")). It is to note that E interactions are not available in OmnipathR.
static_table("annotations", "PROGENy") #> # A tibble: 233,413 × 6 #> uniprot genesymbol entity_type pathway weight p_value #> <chr> <chr> <chr> <chr> <dbl> <dbl> #> 1 P35250 RFC2 protein EGFR 1.47 0.00166 #> 2 P35250 RFC2 protein Androgen -1.28 0.121 #> 3 P35250 RFC2 protein Hypoxia -2.05 0.000704 #> 4 P35250 RFC2 protein Estrogen 2.41 0.0238 #> 5 P35250 RFC2 protein PI3K -0.239 0.804 #> 6 P35250 RFC2 protein WNT 0.466 0.705 #> 7 P35250 RFC2 protein Trail -0.801 0.624 #> 8 P35250 RFC2 protein VEGF -0.157 0.848 #> 9 P35250 RFC2 protein TGFb -0.431 0.630 #> 10 P35250 RFC2 protein NFkB -0.410 0.372 #> # ℹ 233,403 more rows