getCorum: Obtain CORUM protein complex data

In ccb-hms/BioPlex: R-side access to BioPlex protein-protein interaction data

Obtain CORUM protein complex data

Description

Functionality for retrieving the CORUM protein complex data. Available complex collections include:

• complete set of complexes,

• core set of complexes,

• complexes with splice variants.

See references.

Usage

getCorum(
  set = c("all", "core", "splice"),
  organism = "Human",
  remap.uniprot.ids = FALSE,
  cache = TRUE,
  mode = c("ehub", "web")
)

Arguments

set	character. Valid options include: "all": complete set of complexes, "core": core set of complexes, "splice": complexes with splice variants. Defaults to "all".
organism	character. Use NULL to not subset by organism. Defaults to "Human" which restricts the data to human protein complexes only.
remap.uniprot.ids	logical. Should the protein-to-gene mappings from CORUM (i.e. UNIPROT-to-SYMBOL and UNIPROT-to-ENTREZID) be updated using Bioc annotation functionality? Currently only supported in combination with organism = "Human". Defaults to FALSE which will then keep the mappings provided by CORUM.
cache	logical. Should a locally cached version used if available? Defaults to TRUE.
mode	character. Should CORUM complexes be obtained from ExperimentHub or via a web download from the CORUM homepage? Defaults to "ehub", which will obtain the chosen complex set from ExperimentHub.

Value

A data.frame.

References

CORUM: http://mips.helmholtz-muenchen.de/corum/#download

Examples

# Obtain the core set of CORUM complexes
core <- getCorum(set = "core")

ccb-hms/BioPlex documentation built on Aug. 5, 2023, 9:15 p.m.