getPPIbyName: Extract the PPIs for my list of genes defined by Gene name

Description Usage Arguments Value See Also Examples

View source: R/ppiTables.R

Description

Get Protein-Protein interactions (PPIs) for the set of gene names. Function lookups for PPIs for the list of GeneIDs and returns either “induced” (all interaction for this GeneID) or “limited” (only interactions between GeneIDs specified in the query) table of interacting genes A and B, where A and B are respective gene names.

Usage

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getPPIbyName(name, type = c("induced", "limited"))

Arguments

name

Gene names

type

type of the PPI network should be either induced (for all the PPIs for specific genes, including external genes) or limited (for PPIs between the genes specified in the query). Type could be shortened to recognizable minimum like 'ind' or 'lim'.

Value

data.frame with interactors internal GeneID in columns A and B

See Also

getPPIbyEntrez() and getPPIbyIDs() to get PPI data.frame, getIGraphFromPPI() to get igraph representation of the PPI data.frame and getTableFromPPI() to get interpretable table representation of the PPI data.frame.

Other PPI functions: getIGraphFromPPI(), getPPIbyEntrez(), getPPIbyIDs4BrainRegion(), getPPIbyIDs4Compartment(), getPPIbyIDs(), getTableFromPPI()

Examples

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t <- getPPIbyName(
    c("CASK", "DLG4", "GRIN2A", "GRIN2B", "GRIN1"),
    type = "lim"
)

lptolik/synaptome.db documentation built on Dec. 21, 2021, 11:50 a.m.