getBioPlex | R Documentation |
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.
getBioPlex(
cell.line = c("293T", "HCT116"),
version = c("3.0", "1.0", "2.0"),
remap.uniprot.ids = FALSE,
cache = TRUE
)
cell.line |
character. Valid options include:
Defaults to |
version |
character. Valid options include |
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 |
cache |
logical. Should a locally cached version used if available?
Defaults to |
A data.frame
.
BioPlex: https://bioplex.hms.harvard.edu/interactions.php
# (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")
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