Function to find common ancestors of two terms/nodes from a direct acyclic graph (DAG)

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 1.0.11) has been loaded into the working environment (at 2017-03-27 19:53:33)
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:0012705 and HP:0011428 (2017-03-27 19:53:33)...
[1] "HP:0000118"

Source code

dDAGancestor.r

Source man

dDAGancestor.Rd dDAGancestor.pdf

See also

dDAGinduce