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Retrieve a static table from OmniPath

Source: R/static.R
static_table.Rd

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.

Usage

static_table(
  query,
  resource,
  organism = 9606L,
  strict_evidences = TRUE,
  wide = TRUE,
  dorothea_levels = c("A", "B", "C")
)

Arguments

query

Character: a query type such as "annotations" or "interactions".

resource

Character: name of the resource or dataset, such as "CollecTRI" or "PROGENy".

organism

Integer: NCBI Taxonomy of the organism: 9606 for human, 10090 for mouse and 10116 for rat.

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.

wide

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 pivot_annotations.

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 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.

Value

A data frame (tibble) with the requested resource.

See also

static_tables

Examples

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