find_nodes: Search for nodes by name or semantic type

In rsemmed: An interface to the Semantic MEDLINE database

Description

Search for nodes by name (exact match or using regular expressions) or which match supplied semantic types. Perform anti-matching by setting match = FALSE. Capitalization is ignored.

Usage

find_nodes(obj, pattern = NULL, names = NULL, semtypes = NULL, match = TRUE)

Arguments

obj	Either the SemMed graph or a node set (igraph.vs)
pattern	Regular expression used to find matches in node names
names	Character vector of exact node names
semtypes	Character vector of semantic types
match	If TRUE, return nodes that DO match pattern (default). If FALSE, return nodes that DO NOT match.

Value

A vertex sequence of matching nodes

Examples

data(g_mini)
find_nodes(g_mini, pattern = "cortisol")
find_nodes(g_mini, pattern = "cortisol$")
find_nodes(g_mini, pattern = "stress")
find_nodes(g_mini, pattern = "stress") %>%
    find_nodes(pattern = "disorder", match = FALSE)

find_nodes(g_mini, names = "Serum cortisol")
find_nodes(g_mini, names = "Chronic Stress")

find_nodes(g_mini, semtypes = "dsyn")
find_nodes(g_mini, semtypes = c("dsyn", "fndg"))

## pattern and semtypes are combined via OR:
find_nodes(g_mini, pattern = "cortisol", semtypes = "horm")

## To make an AND query, chain find_nodes sequenctially:
find_nodes(g_mini, pattern = "cortisol") %>%
    find_nodes(semtypes = "horm")

rsemmed documentation built on Nov. 8, 2020, 5:32 p.m.