find_limit: Finds the limit cutoff when target and sentinal paths are...

In jgockley62/igraphNetworkExpansion: Trace Subnetworks from an AD Necortical Network of Protein-Protein Interactions

Finds the limit cutoff when target and sentinal paths are given

Description

Limit is based on whichever value is greater between; the mean or median scores of the Target-traced-to-sentinal paths. If there are no target to sentinal paths the pairwise within target traces are used.

Usage

find_limit(s_path, t_path, weights, cores = 1)

Arguments

s_path	the sentinel path object
t_path	the target path object
weights	OMICS/vertex scores as named vector
cores	the cores to run the path calulation over. default = 1

Value

List object with named attributes of limit (the path score cutoff limit) and both t_verts and s_verts objects used as placeholders to determine if the paths were scorable.

Examples

example_path <- list()
example_path$res <- list(
   c('319', "49", "23", "86", "690", "238"),
   c('422', "899", "37", "240", "970", "28")
)
names(example_path$res[[1]]) <- c(
   "GeneA","GeneZ", "GeneAlpha",
   "GeneB", "GeneX", "GeneOmega"
)
names(example_path$res[[2]]) <- c(
   "Gene1","Gene2", "GeneUno",
   "Gene12", "Gene13", "GeneOcho"
)
example_path_b <-  example_path 
sampweights <- c(1.45, 2.45, 0.89, .003, 1.3, 2.1, 0.02, 0, 0, 0.2, 0.6, .70)
names(sampweights) <- c(
   "GeneA","GeneZ", "GeneAlpha",
   "GeneB", "GeneX", "GeneOmega",
   "Gene1","Gene2", "GeneUno",
   "Gene12", "Gene13", "GeneOcho"
)
find_limit(
   s_path = example_path,
   t_path =  example_path_b,
   weights = sampweights,
   cores = 2
)

jgockley62/igraphNetworkExpansion documentation built on April 15, 2022, 12:14 a.m.