RWR_LOE: RWR LOE

In dkainer/RWRtoolkit: Random Walk with Restart Tool Suite

RWR LOE

Description

RWR_LOE perform RWR lines-of-evidence. RWR_LOE has two possible functions. Given one geneset of seeds, rankings for all other genes in the network will be returned. Given a second geneset of genes to be queried, ranking for just the genes in that geneset will be returned. This can be used to build multiple lines of evidence from the various input networks to relate the two gene sets.

Usage

RWR_LOE(
  data = NULL,
  seed_geneset = NULL,
  query_geneset = NULL,
  restart = 0.7,
  tau = "1.0",
  outdir = "./",
  numranked = 1,
  plot = FALSE,
  modname = "default",
  cyto = 0,
  verbose = FALSE
)

Arguments

data	The path to the Rdata object generated from RWR_make_multiplex
seed_geneset	The path to the gene set file. It must have the following first two columns with no headers tab-delimited: <setid> <gene> <weight>
query_geneset	The path to the optional second gene set file. It must have the following first two columns with no headers tab-delimited: <setid> <gene> <weight>
restart	Sets the restart parameter [0,1). Higher value means the walker will jump back to a seed node more often. Defaulted to 0.7
tau	Comma-separated list of values between that MUST add up to the number of network layers in the .Rdata file. One value per network layer that determines the probability that the random walker will restart in that layer. e.g. if there are three layers (A,B,C) in your multiplex network, then –tau '0.2,1.3,1.5' will mean that layer A is less likely to be walked on after a restart than layers B or C. Default 1.0
outdir	Full path to the output file directory
numranked	Proprtion of ranked genes to return [0,1]. e.g. 0.1 will return the top 10%. Default 1.0
plot	Output PNG plot of ROC and PRC of the query geneset with respect the seed geneset.
modname	String to include in output file name. Default "default"
cyto	Specify a number N > 0 if you wish to see a network of the seeds and top N ranked genes (cytoscape must already be running)
verbose	Verbose mode (Default False)

Value

Returns a list of: (1) a dataframe of results (scores for genes) and (2) the seed genes.

Examples

# An example of a default RWR LOE with one geneset which will
# return a ranked list

extdata.dir <- system.file("example_data", package = "RWRtoolkit")
multiplex_object_filepath <- paste(
  extdata.dir,
  "/string_interactions.Rdata",
  sep = ""
)
geneset1_filepath <- paste(extdata.dir, "/geneset1.tsv", sep = "")
geneset2_filepath <- paste(extdata.dir, "/geneset2.tsv", sep = "")
outdir <- "./rwr_loe"

# for all other genes in the network
loe_gene_seed_list <- RWR_LOE(
  data = multiplex_object_filepath,
  seed_geneset = geneset1_filepath,
  tau = "1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0",
  outdir = outdir
)

# An example of an RWR LOE with two genesets, the first defines the seeds
# and the output will be rankings for the genes in the second geneset
loe_gene_seed_list2 <- RWR_LOE(
  data = multiplex_object_filepath,
  seed_geneset = geneset1_filepath,
  query_geneset = geneset2_filepath,
  tau = "1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0",
  outdir = outdir
)

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