Calculate a pathway space distance between two vectors

Usage

pathDistances(gdist, from, to, nperm = 1000, verbose = TRUE)

Arguments

gdist: A distance matrix computed by the igraph's distances function. Rows and columns must be named with vertex labels as listed in the 'igraph' object.
from: A vector with valid vertex names.
to: A vector with valid vertex names.
nperm: Number of permutations.
verbose: A single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Value

A list with pathway space distances and a 'ggplot' object.

Examples


# Load a vertex-wise distance matrix (distance between nodes in a graph)
data("gdist.toy", package = "PathwaySpace")

# Get two vertex lists
from <- sample(colnames(gdist.toy), 50)
to <- sample(colnames(gdist.toy), 50)

# Calculate distances between lists, and between random lists
res <- pathDistances(gdist.toy, from, to)
#> Computing pathway distance...
#> Running permutation analysis...
#> 
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names(res)
#> [1] "p_dist"  "z_score"
# "p_dist"  "z_score"

Calculate a pathway space distance between two vectors

Usage

Arguments

Value

See also

Examples