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Add API using plumber

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Elias Projahn 2022-12-11 19:08:22 +01:00
parent 26a209aade
commit 7f70a0c90b
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inst/plumber/ubigen/plumber.R Normal file
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# This file contains an API specification for Ubigen that can be served using
# the `plumber` package.
library(data.table)
library(plumber)
#' Retrieve a ranking of genes based on their ubiquity.
#'
#' Provide a whitespace separated list of gene IDs as the request content to
#' filter the results based on these genes.
#'
#' @param dataset The predefined dataset to use. This may be one of
#' `gtex_all`, `gtex_tissues` or `hpa_tissues`.
#'
#' @get /ranking
#' @post /ranking
#' @parser text
#' @serializer csv
ranking <- function(req,
dataset = "gtex_all",
cross_sample_metric = "above_95",
cross_sample_weight = 0.5,
level_metric = "median_expression_normalized",
level_weight = 0.25,
variation_metric = "qcv_expression_normalized",
variation_weight = -0.25) {
ranking <- ubigen::rank_genes(
data = {
analysis <- if (dataset == "gtex_tissues") {
ubigen::gtex_tissues
} else if (dataset == "hpa_tissues") {
ubigen::hpa_tissues
} else {
ubigen::gtex_all
}
merge(analysis, ubigen::genes, by = "gene")
},
cross_sample_metric = cross_sample_metric,
cross_sample_weight = as.numeric(cross_sample_weight),
level_metric = level_metric,
level_weight = as.numeric(level_weight),
variation_metric = variation_metric,
variation_weight = as.numeric(variation_weight)
)
if (length(req$body) >= 1) {
inputs <- unique(strsplit(req$body, "\\s+")[[1]])
inputs <- inputs[inputs != ""]
ranking[gene %chin% inputs]
} else {
ranking
}
}
#' Get a summary of the ubiquity of a given gene set.
#'
#' Provide a whitespace separated list of gene IDs as the request content to
#' analyze these genes.
#'
#' @param dataset The predefined dataset to use. This may be one of
#' `gtex_all`, `gtex_tissues` or `hpa_tissues`.
#'
#' @post /summary
#' @parser text
#' @serializer json
summary <- function(req,
res,
dataset = "gtex_all",
cross_sample_metric = "above_95",
cross_sample_weight = 0.5,
level_metric = "median_expression_normalized",
level_weight = 0.25,
variation_metric = "qcv_expression_normalized",
variation_weight = -0.25) {
ranking <- ubigen::rank_genes(
data = {
analysis <- if (dataset == "gtex_tissues") {
ubigen::gtex_tissues
} else if (dataset == "hpa_tissues") {
ubigen::hpa_tissues
} else {
ubigen::gtex_all
}
merge(analysis, ubigen::genes, by = "gene")
},
cross_sample_metric = cross_sample_metric,
cross_sample_weight = as.numeric(cross_sample_weight),
level_metric = level_metric,
level_weight = as.numeric(level_weight),
variation_metric = variation_metric,
variation_weight = as.numeric(variation_weight)
)
if (length(req$body) >= 1) {
inputs <- unique(strsplit(req$body, "\\s+")[[1]])
inputs <- inputs[inputs != ""]
reference_scores <- ranking[!gene %chin% inputs, score]
comparison_score <- ranking[gene %chin% inputs, score]
comparison_percentile <- ranking[gene %chin% inputs, percentile]
test_result <- stats::wilcox.test(
x = comparison_score,
y = reference_scores,
conf.int = TRUE
)
list(
"median_percentile" = stats::median(comparison_percentile) |>
jsonlite::unbox(),
"median_score" = stats::median(comparison_score) |>
jsonlite::unbox(),
"median_score_reference" = stats::median(reference_scores) |>
jsonlite::unbox(),
"p_value" = test_result$p.value |> jsonlite::unbox(),
"change" = test_result$estimate |> jsonlite::unbox(),
"conf_int_lower" = test_result$conf.int[1] |> jsonlite::unbox(),
"conf_int_upper" = test_result$conf.int[2] |> jsonlite::unbox()
)
} else {
res$status <- 400
paste0(
"Please provide a whitespace separated list of Ensembl gene IDs ",
"in the request body."
) |> jsonlite::unbox()
}
}