getBioPlex: Obtain BioPlex protein-protein interaction data

View source: R/bioplex.R

getBioPlexR Documentation

Obtain BioPlex protein-protein interaction data

Description

Functionality for retrieving the BioPlex protein-protein interaction data. Available networks include:

  • BioPlex 293T cells (versions 1.0, 2.0, and 3.0),

  • BioPlex HCT116 cells (version 1.0).

See references.

Usage

getBioPlex(
  cell.line = c("293T", "HCT116"),
  version = c("3.0", "1.0", "2.0"),
  remap.uniprot.ids = FALSE,
  cache = TRUE
)

Arguments

cell.line

character. Valid options include:

  • "293T": derivative of human embryonic kidney 293 cell line,

  • "HCT116": human colon cancer cell line 116.

Defaults to "293T".

version

character. Valid options include "1.0", "2.0", and "3.0" for 293T cells. For HCT116 cells, only "1.0" is available. Defaults to "3.0".

remap.uniprot.ids

logical. Should the protein-to-gene mappings from BioPlex (i.e. UNIPROT-to-SYMBOL and UNIPROT-to-ENTREZID) be updated using Bioc annotation functionality? Defaults to FALSE which will then keep the mappings provided by BioPlex.

cache

logical. Should a locally cached version used if available? Defaults to TRUE.

Value

A data.frame.

References

BioPlex: https://bioplex.hms.harvard.edu/interactions.php

Examples

# (1) Obtain the latest version of the 293T PPI network
bp.293t <- getBioPlex(cell.line = "293T", version = "3.0")

# (2) Obtain the latest version of the HCT116 PPI network
bp.hct116 <- getBioPlex(cell.line = "HCT116", version = "1.0")

ccb-hms/BioPlex documentation built on July 20, 2022, 9:16 a.m.