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

In paxtoolsr: PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons

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)

paxtoolsr documentation built on Nov. 8, 2020, 8:29 p.m.