dDAGancestor: Function to find common ancestors of two terms/nodes from a...

In dnet: Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

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

See Also

dDAGinduce

Examples

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

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: supraHex
Loading required package: hexbin
'ig.HPPA' (from package 'dnet' version 1.1.4) has been loaded into the working environment (at 2020-01-13 14:28:15)
Find common ancestors shared by HP:0011991 and HP:0008421 (2020-01-13 14:28:15)...
[1] "HP:0000118"

dnet documentation built on Feb. 20, 2020, 3:01 p.m.