getShortestPathSif: Get the shortest between two IDs (HGNC or CHEBI)

In BioPAX/paxtoolsr: Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Get the shortest between two IDs (HGNC or CHEBI)

Description

Get the shortest between two IDs (HGNC or CHEBI)

Usage

getShortestPathSif(
  sif,
  idA,
  idB,
  mode = c("all", "out", "in"),
  weights = NULL,
  verbose = FALSE,
  filterFun,
  ...
)

Arguments

sif	a SIF network
idA	HGNC or CHEBI (CHEBI:XXXXX) ID
idB	HGNC or CHEBI (CHEBI:XXXXX) ID
mode	see shortest_paths() in igraph
weights	see shortest_paths() in igraph
verbose	a boolean whether to show debugging information
filterFun	a function to filter multiple paths of the same length
...	additional arguments passed on to filterFun

Value

a data.frame representing a SIF network

Examples

idA <- "DAP3"
idB <- "RPS16"
sif <- readSif(system.file("extdata", "test_sif_shortestPath.txt", package="paxtoolsr"))
filterFun <- function(vpaths) { idx <- sample(1:length(vpaths), 1); return(vpaths[[idx]]) }
m1 <- getShortestPathSif(sif, idA, idB, mode="all", weights=NULL, filterFun=filterFun, verbose=TRUE)

BioPAX/paxtoolsr documentation built on Jan. 31, 2023, 4:22 a.m.