nomenCheckup: repair nomenclature mismatches (to curated term set) in a...
In ontoProc: processing of ontologies of anatomy, cell lines, and so on

Description Usage Arguments Value Examples

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

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

`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`

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.

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")