getPPIbyIDs4BrainRegion: Prepare induced or limited network for brain region

In lptolik/synaptome.db: Synamptosome Proteome Database

Prepare induced or limited network for brain region

Description

Prepare PPI network for genes from your list annotated for specific brain region. Should be used with findGenesByEntrez()) or findGenesByName() functions to obtain list of internal IDs for your list of genes. Could be used with getAllGenes4BrainRegion functions to obtain all genes belonging to respective brain region. Function lookups the PPI table for gene IDs from the list and returns “limited” or “induced” interactors GeneIDs for the specified region.

Usage

getPPIbyIDs4BrainRegion(
  ids,
  brainRegion,
  taxID,
  type = c("induced", "limited")
)

Arguments

ids	gene IDs
brainRegion	region ID
taxID	taxon ID
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

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

Other BrainRegion functions: getAllGenes4BrainRegion(), getBrainRegions(), getGenes4BrainRegion()

Examples

# getting all genes for mouse Striatum
gns <- getAllGenes4BrainRegion(brainRegion = "Striatum", taxID = 10090)
head(gns)

# getting full PPI network for postsynaptic compartment
ppi <- getPPIbyIDs4BrainRegion(
    gns$GeneID,
    brainRegion = "Striatum",
    taxID = 10090,
    type = "limited"
)
head(ppi)

lptolik/synaptome.db documentation built on Sept. 13, 2023, 2:50 p.m.