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

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.

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
)
#> Working on: GRIN2B
#> 313 target paths out of 536 ( 58.4% ) kept
#> 42 of 137 target genes ( 30.66% ) filtered out
#> 316 sentinel paths out of 646 ( 48.92% ) kept
#> 48 of 180 sentinel genes ( 26.67% ) filtered out