Removing concept of group thresholds from gpmapr (#5)

Author: andrew-e

R/genes.R

@@ -3,7 +3,6 @@
 #' @param gene_id A numeric value specifying the gene id
 #' @param include_associations A logical value specifying whether to include associations
 #' (BETA, SE, P), defaults to FALSE
-#' @param coloc_group_threshold A character value specifying the group threshold for coloc groups, defaults to 'strong'
 #' @param include_coloc_pairs A logical value specifying whether to include coloc pairs, defaults to FALSE
 #' @param h4_threshold A numeric value specifying the h4 threshold for coloc pairs, defaults to 0.8
 #' @return A list which contains the following elements:
@@ -28,17 +27,12 @@
 #' @export
 gene <- function(gene_id,
                  include_associations = FALSE,
-                 coloc_group_threshold = "strong",
                  include_coloc_pairs = FALSE,
                  h4_threshold = 0.8) {
   if (is.null(gene_id)) {
     stop("gene_id is required")
   }
-  if (!coloc_group_threshold %in% c("strong", "moderate")) {
-    stop("coloc_group_threshold must be either 'strong' or 'moderate'")
-  }
   gene_info <- gene_api(gene_id, include_associations, include_coloc_pairs, h4_threshold)
-  gene_info$coloc_groups <- dplyr::filter(gene_info$coloc_groups, group_threshold == coloc_group_threshold)
   gene_info$tissues <- NULL
 
   gene_info <- cleanup_api_object(gene_info)

R/region.R

@@ -3,7 +3,6 @@
 #' @param region_id A numeric value specifying the region id
 #' @param include_associations A logical value specifying whether to include associations
 #' (BETA, SE, P), defaults to FALSE
-#' @param coloc_group_threshold A character value specifying the group threshold for coloc groups, defaults to 'strong'
 #' @param include_coloc_pairs A logical value specifying whether to include coloc pairs, defaults to FALSE
 #' @param h4_threshold A numeric value specifying the h4 threshold for coloc pairs, defaults to 0.8
 #' @return A list which contains the following elements:
@@ -29,17 +28,12 @@
 #' @export
 region <- function(region_id,
                    include_associations = FALSE,
-                   coloc_group_threshold = "strong",
                    include_coloc_pairs = FALSE,
                    h4_threshold = 0.8) {
   if (is.null(region_id)) {
     stop("region_id is required")
   }
-  if (!coloc_group_threshold %in% c("strong", "moderate")) {
-    stop("coloc_group_threshold must be either 'strong' or 'moderate'")
-  }
   region_info <- region_api(region_id, include_associations, include_coloc_pairs, h4_threshold)
-  region_info$coloc_groups <- dplyr::filter(region_info$coloc_groups, group_threshold == coloc_group_threshold)
 
   region_info <- cleanup_api_object(region_info)
   region_info <- merge_associations(region_info)

R/traits.R

@@ -4,7 +4,6 @@
 #' @param trait_id A numeric value specifying the trait id
 #' @param include_associations A logical value specifying whether to include associations
 #' (BETA, SE, P), defaults to FALSE
-#' @param coloc_group_threshold A character value specifying the group threshold for coloc groups, defaults to 'strong'
 #' @param include_coloc_pairs A logical value specifying whether to include coloc pairs, defaults to FALSE
 #' @param h4_threshold A numeric value specifying the h4 threshold for coloc pairs, defaults to 0.8
 #' @return A list which contains the following elements:
@@ -29,18 +28,13 @@
 #' @export
 trait <- function(trait_id,
                   include_associations = FALSE,
-                  coloc_group_threshold = "strong",
                   include_coloc_pairs = FALSE,
                   h4_threshold = 0.8) {
   if (is.null(trait_id)) {
     stop("trait_id is required")
   }
-  if (!coloc_group_threshold %in% c("strong", "moderate")) {
-    stop("coloc_group_threshold must be either 'strong' or 'moderate'")
-  }
 
   trait_info <- trait_api(trait_id, include_associations, include_coloc_pairs, h4_threshold)
-  trait_info$coloc_groups <- dplyr::filter(trait_info$coloc_groups, group_threshold == coloc_group_threshold)
 
   trait_info <- cleanup_api_object(trait_info)
   if (include_associations) trait_info <- merge_associations(trait_info)

R/variants.R

@@ -1,7 +1,6 @@
 #' @title Variant
 #' @description A collection of studies that are associated with a particular variant.
 #' @param snp_id A character string specifying the SNP ID
-#' @param coloc_group_threshold A character value specifying the group threshold for coloc groups, defaults to 'strong'
 #' @param include_coloc_pairs A logical value specifying whether to include coloc pairs
 #' @param h4_threshold A numeric value specifying the cutoff for included coloc pairs, defaults to 0.8.
 #'      Only used if include_coloc_pairs is TRUE.
@@ -25,19 +24,14 @@
 #' @inheritSection coloc_pairs_doc coloc_pairs_dataframe
 #' @export
 variant <- function(snp_id,
-                    coloc_group_threshold = "strong",
                     include_coloc_pairs = FALSE,
                     h4_threshold = 0.8,
                     include_summary_stats = FALSE) {
   if (is.null(snp_id)) {
     stop("snp_id is required")
   }
-  if (!coloc_group_threshold %in% c("strong", "moderate")) {
-    stop("coloc_group_threshold must be either 'strong' or 'moderate'")
-  }
 
   variant_info <- variant_api(snp_id, include_coloc_pairs = include_coloc_pairs, h4_threshold = h4_threshold)
-  variant_info$coloc_groups <- dplyr::filter(variant_info$coloc_groups, group_threshold == coloc_group_threshold)
 
   if (include_summary_stats) {
     summary_stats <- variant_summary_stats_api(snp_id)

man/cleanup_api_object.Rd

@@ -65,7 +65,6 @@ You can get more information about a trait by subsequently calling the `trait()`
 Each trait, gene, or variant call have optional parameters:
 
 * `include_associations`: Whether to include associations (BETA, SE, P) of the variants in which it's colocalised in the output.
-* `group_threshold`: The threshold for coloc groups, can be 'strong' (h4 > 0.8) or 'moderate' (h4 > 0.6), defaults to 'strong'.
 * `include_coloc_pairs`: Whether to include coloc pairs in the output (which include h3 and h4), as opposed to just the coloc groups.
 * `h4_threshold`: The h4 threshold for coloc pairs.
 
@@ -85,10 +84,10 @@ This returns a list of elements, which you can access by name.  More detailed ex
 * `coloc_pairs`: (optional) a dataframe containing all pairwise coloc results for this trait.
 
 ```{r gene-example}
-slc44a1 <- gene("SLC44A1", coloc_group_threshold = "moderate")
+slc44a1 <- gene("SLC44A1")
 names(slc44a1)
 nrow(slc44a1$coloc_groups)
-head(slc44a1$coloc_groups[, c("coloc_group_id", "group_threshold", "trait_name", "data_type", "tissue")])
+head(slc44a1$coloc_groups[, c("coloc_group_id", "trait_name", "data_type", "tissue")])
 ```
 
 # Accessing summary statistics