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.
find_limit(s_path, t_path, weights, cores = 1)
| 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 |
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.
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 )#> $cutoff #> Median #> 0.780375 #> #> $t_verts #> [1] 0 0 0 #> #> $s_verts #> [1] 0 0 0 #>