nomenCheckup {ontoProc} | R Documentation

## 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")

[Package ontoProc version 1.6.0 Index]