Turn an IMPC phenotype response into a table — impc_parse

Pure.

Usage

impc_parse_phenotypes(body, mgi = NA_character_)

Arguments

body: A parsed IMPC genotype-phenotype/select response.
mgi: The MGI marker accession that was queried.

Value

A tibble of mp_id, mp_name, allele, allele_symbol, zygosity, and source_url, one row per distinct phenotype term. NULL when there are none.

One row per term, not per observation

IMPC reports a document per phenotype, sex, zygosity, and parameter combination, so the same term recurs many times over. Rows are collapsed to distinct mp_id, keeping the first occurrence. Counting the raw documents would report a gene's phenotype breadth several times over.

mp_id is an MP term for most phenotypes and an MPATH term for pathology findings. Both appear in the same field.

Examples

body <- list(response = list(docs = list(
  list(
    mp_term_id = "MP:0011100",
    mp_term_name = "preweaning lethality, complete penetrance",
    allele_accession_id = "MGI:4364806",
    zygosity = "homozygote"
  )
)))
impc_parse_phenotypes(body, "MGI:97306")
#> # A tibble: 1 × 6
#>   mp_id      mp_name                    allele allele_symbol zygosity source_url
#>   <chr>      <chr>                      <chr>  <chr>         <chr>    <chr>     
#> 1 MP:0011100 preweaning lethality, com… MGI:4… NA            homozyg… https://w…