diff --git a/R/alliance.R b/R/alliance.R index a4a46b33..27e87ce5 100644 --- a/R/alliance.R +++ b/R/alliance.R @@ -65,14 +65,16 @@ read_alliance <- function(alliance_tsv) { #' #' @param alliance_tbl a dataframe derived from Alliance data (usually a #' [downloaded .tsv file](https://www.alliancegenome.org/downloads)) -#' @param term_subset character vector of DOIDs to limit counts to +#' @param term_subset character vector of DOIDs to limit counts to (default: NULL) #' @param by_type logical indicating whether to count by Alliance object type -#' (i.e. gene, allele, model) +#' (i.e. gene, allele, model) (default: TRUE) #' @param pivot logical indicating whether to pivot values to type columns; -#' ignored if by_type = FALSE. -#' @param record_lvl a string indicating the desired specificity of records. +#' ignored if by_type = FALSE (default: TRUE) +#' @param record_lvl a string indicating the desired specificity of records; +#' see details for options (default: "disease-object") #' @param assign_to how to assign records when counting; one of "species" or #' "curator" (i.e. the organization responsible for curating the record) +#' (default: "species") #' #' @return #' A summary tibble with the count of unique object annotations defined by diff --git a/man/count_alliance_records.Rd b/man/count_alliance_records.Rd index dd4b8b49..8ff586a8 100644 --- a/man/count_alliance_records.Rd +++ b/man/count_alliance_records.Rd @@ -17,18 +17,20 @@ count_alliance_records( \item{alliance_tbl}{a dataframe derived from Alliance data (usually a \href{https://www.alliancegenome.org/downloads}{downloaded .tsv file})} -\item{term_subset}{character vector of DOIDs to limit counts to} +\item{term_subset}{character vector of DOIDs to limit counts to (default: NULL)} \item{by_type}{logical indicating whether to count by Alliance object type -(i.e. gene, allele, model)} +(i.e. gene, allele, model) (default: TRUE)} \item{pivot}{logical indicating whether to pivot values to type columns; -ignored if by_type = FALSE.} +ignored if by_type = FALSE (default: TRUE)} -\item{record_lvl}{a string indicating the desired specificity of records.} +\item{record_lvl}{a string indicating the desired specificity of records; +see details for options (default: "disease-object")} \item{assign_to}{how to assign records when counting; one of "species" or -"curator" (i.e. the organization responsible for curating the record)} +"curator" (i.e. the organization responsible for curating the record) +(default: "species")} } \value{ A summary tibble with the count of unique object annotations defined by