Description

dDAGancestor is supposed to find a list of common ancestors shared by two terms/nodes, given a direct acyclic graph (DAG; an ontology). If two terms are given as NULL, then a sparse matrix of children x ancestors is built for all terms. If one of them is null, then a sparse matrix of children x ancestors is built but only for non-null input terms.

Usage

dDAGancestor(g, term1 = NULL, term2 = NULL, verbose = T)

Arguments

g

an object of class "igraph" or "graphNEL"

term1

the first term/node as input

term2

the second term/node as input

verbose

logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display

Value

• When two terms are given: a list of terms/nodes that are common ancestors for two input terms/nodes
• When two terms are given as NULL: a sparse matrix of children x ancestors is built for all terms, with '1' for the reachable and otherwise '0'.
• When one of terms is given as NULL: a sparse matrix of children x ancestors is built but only for non-null input terms, with '1' for the reachable and otherwise '0'.

Note

none

Examples

# 1) load HPPA as igraph object
ig.HPPA <-dRDataLoader(RData='ig.HPPA')

'ig.HPPA' (from package 'dnet' version 1.1.2) has been loaded into the working environment (at 2018-01-19 12:34:33)
g <- ig.HPPA

# 2) randomly give two terms
term1 <- sample(V(g)$name,1)
term2 <- sample(V(g)$name,1)

# 3) find common ancestors
dDAGancestor(g, term1, term2)

Find common ancestors shared by HP:0002152 and HP:0009523 (2018-01-19 12:34:33)...
[1] "HP:0000118"

Source code

Source man

See also