static_table: Retrieve a static table from OmniPath
In saezlab/OmnipathR: OmniPath web service client and more

static_table

R Documentation

Retrieve a static table from OmniPath

Description

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.