short_paths: Traces the shortest paths of a gene to a vector of Target...

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

Traces the shortest paths of a gene to a vector of Target Gene and a vector of Sentinal Genes

Description

Traces the the shortest paths of target gene paiwise to the target gene list. then traces the shortest path of the gene to a list of sentinal genes. This function returns the list of genes in a path object which score over the an emperically defined limit using the find_limit() function.

Usage

short_paths(tnet, target, targets, sentinals, cores = 1)

Arguments

tnet	igraph network (Main entire network) eg. net/net_undirected/JS_net_undirected
target	the from gene target eg Genes[1]
targets	List of the total list of targets in the User set eg. Genes
sentinals	List of the sentinal genes to trace to eg. Sentinal
cores	the number of cores to use in paralellizable functions

Value

List object of Inter genes from target path traces and Sentinal genes from sentinal gene traces

Examples

 
data(slim_net, package = "igraphNetworkExpansion")
data(genelists, package = "igraphNetworkExpansion")

example_path <- short_paths(
    tnet = slim_net,
    target = genelists$targets$APP_Metabolism[1],
    targets = genelists$targets$APP_Metabolism,
    sentinals = genelists$sentinals$Immune_Response,
    cores = 1
)

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