RWR_make_multiplex: RWR Make Multiplex

In dkainer/RWRtoolkit: Random Walk with Restart Tool Suite

RWR Make Multiplex

Description

RWR_make_multiplex creates a multiplex network.

Usage

RWR_make_multiplex(
  flist = "",
  delta = 0.5,
  output = "network.Rdata",
  verbose = FALSE
)

Arguments

flist	Table describing network files to use. File columns: <path to file> <short name of network>. <group>. 'groups' are either 1, 2, or 3. All 1's will form one multiplex network (e.g. gene-to-gene), All 2's will form a separate multiplex network (e.g. disease-to-disease), And all 3's will be used to join the 1's and 2's together (e.g. gene-to-disease) You don't have to have both 1's and 2's. But if you do have 1's and 2's, you SHOULD have at least one 3 to join them up. Can be delimited by comma, tab, space, pipe, or semicolon.
delta	Probability to change between layers at the next step [0,1]. If delta = 0, the particle will always remain in the same layer after a non-restart iteration. If delta = 1, the particle will always change between layers, therefore not following the specific edges of each layer. Default is 0.5.
output	Output file name (default "network.Rdata")
verbose	Verbose mode. Default FALSE
test	Runs an example. Default FALSE

Value

Mutliplex object is saved to a file (.rdata) to load into subsequent functions.

Examples

#
# An example of a default RWR Make Multiplex with an output "network.Rdata"
extdata.dir <- system.file("example_data", package = "RWRtoolkit")
outdir <- "./rwr_make_multiplex"

layers.path <- paste(extdata.dir, "/layers/", sep = "")
layers <- list.files(layers.path)
layer_with_paths <- paste(layers.path, layers, sep = "")
layer_names <- sub(pattern = "(.*)\\..*$",
                   replacement = "\\1", basename(layers))
groups <- rep(1, length(layer_names))
flistdatatable <- data.table::data.table(layer_with_paths,
                                         layer_names,
                                         groups)

outfile <- paste(outdir, "/multiplex.Rdata", sep = "")
write.table(flistdatatable,
  row.names = FALSE,
  col.names = FALSE,
  sep = "\t",
  file = "example.flist", quote = FALSE
)

RWR_make_multiplex(
  flist = "example.flist",
  output = outfile
)



# An example of an RWR Make Multiplex with a non-default delta and
# with a specified output filename.
outfile <- paste(outdir, "/multiplex_d25_l75.Rdata", sep = "")
RWR_make_multiplex(
  flist = "example.flist",
  delta = 0.25,
  output = outfile
)

system("rm example.flist")

dkainer/RWRtoolkit documentation built on Jan. 11, 2025, 3:26 a.m.