nomenCheckup: repair nomenclature mismatches (to curated term set) in a...

In vjcitn/ontoProc: processing of ontologies of anatomy, cell lines, and so on

repair nomenclature mismatches (to curated term set) in a vector of terms

Description

repair nomenclature mismatches (to curated term set) in a vector of terms

Usage

nomenCheckup(cand, namedOffic, n = 1, tagcolname = "tag", ...)

Arguments

cand	character vector of candidate terms
namedOffic	named character vector of curated terms, the names are regarded as tags, intended to be identifiers in curated ontologies
n	numeric(1) number of nearest neighbors to return
tagcolname	character(1) prefix used to name columns for tags in output
...	passed to adist

Value

a data.frame instance with 2n+1 columns (column 1 is candidate, remaining n pairs of columns are (term, tag) for n nearest neighbors as measured by adist.

Examples

candidates = c("JHH7", "HUT102", "HS739T", "NCIH716")
# the candidates are cell line names returned in the text dump from
# https://portals.broadinstitute.org/ccle/page?gene=AHR
# note that one must travel to the third nearest neighbor
# to find the match (and tag) for Hs 739.T
# in this example, we compare to cell line names in Cell Line Ontology
nomenCheckup(candidates, cleanCLOnames(), n=3, tagcolname="clo")

vjcitn/ontoProc documentation built on Oct. 12, 2024, 4:35 p.m.