#' Query Rare Variant Pathway Associations
#'
#' @param datasets A vector of strings
#' @param features A vector of strings
#' @param pathways A vector of strings
#' @param min_p_value A Double
#' @param max_p_value A Double
#' @param paging A named list
#' @param ... Arguments to create_result_from_api_query
#'
#' @export
query_rare_variant_pathway_associations <- function(
datasets = NA,
features = NA,
pathways = NA,
min_p_value = NA,
max_p_value = NA,
paging = NA,
...
){
tbl <- create_result_from_cursor_paginated_api_query(
query_args = list(
"dataSet" = datasets,
"feature" = features,
"pathway" = pathways,
"minPValue" = min_p_value,
"maxPValue" = max_p_value,
"paging" = paging,
"distinct" = F
),
query_file = "rare_variant_pathway_associations.txt",
default_tbl = dplyr::tibble(
"dataset_name" = character(),
"dataset_display" = character(),
"feature_name" = character(),
"feature_display" = character(),
"feature_germline_module" = character(),
"feature_germline_category" = character(),
"pathway" = character(),
"p_value" = double(),
"min" = double(),
"max" = double(),
"mean"= double(),
"q1" = double(),
"q2" = double(),
"q3" = double(),
"n_mutants" = integer(),
"n_total" = integer()
),
select_cols = c(
"dataset_name" = "dataSet.name",
"dataset_display" = "dataSet.display",
"feature_name" = "feature.name",
"feature_display" = "feature.display",
"feature_germline_module" = "feature.germlineModule",
"feature_germline_category" = "feature.germlineCategory",
"pathway",
"p_value" = "pValue",
"min",
"max",
"mean",
"q1",
"q2",
"q3",
"n_mutants" = "nMutants",
"n_total" = "nTotal"
),
...
)
}
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