nomenCheckup {ontoProc} | R Documentation |
repair nomenclature mismatches (to curated term set) in a vector of terms
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 |
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")