Count Alliance Records
count_alliance_records.RdCounts records in data from the Alliance of Genome Resources. Counts can
be ascribed to the species the record is associated with or the Model
Organism Database (MOD) that curated it, optionally by object type.
count_alliance_records() was primarily designed to count records in the
Alliance Disease Associations File. There is no guarantee that any/all
options will work for other files.
Usage
count_alliance_records(
alliance_tbl,
term_subset = NULL,
by_type = TRUE,
pivot = TRUE,
record_lvl = "disease-object",
assign_to = c("species", "curator")
)Arguments
- alliance_tbl
a dataframe derived from Alliance data (usually a downloaded .tsv file)
- term_subset
character vector of DOIDs to limit counts to
- by_type
logical indicating whether to count by Alliance object type (i.e. gene, allele, model)
- pivot
logical indicating whether to pivot values to type columns; ignored if by_type = FALSE.
- record_lvl
a string indicating the desired specificity of records.
- assign_to
how to assign records when counting; one of "species" or "curator" (i.e. the organization responsible for curating the record)
Value
A summary tibble with the count of unique object annotations defined by
record_lvl, aggregated according to species/curator (assign_to) and,
optionally, object type (by_type).
Details
The type of record information to use in counting should be specified with
record_lvl which accepts the following values:
"full_record" counts full non-duplicate records
"disease-object" counts unique disease-object combinations
"disease" counts unique diseases
"object" counts unique MOD objects (i.e. gene, allele, model identifiers)