rm gwasglue2 functions

DESCRIPTION

@@ -11,7 +11,7 @@ Authors@R: c(
     person("Rita", "Rasteiro", , "rita.rasteiro@bristol.ac.uk", role = "aut",
            comment = c(ORCID = "0000-0002-4217-3060"))
     )
-Description: R interface to the 'OpenGWAS' database API. Includes a wrapper
+Description: Interface to the 'OpenGWAS' database API. Includes a wrapper
     to make generic calls to the API, plus convenience functions for
     specific queries.
 License: MIT + file LICENSE
@@ -20,7 +20,6 @@ BugReports: https://github.com/MRCIEU/ieugwasr/issues
 Depends:
     R (>= 4.0)
 Imports:
-    digest,
     dplyr,
     googleAuthR,
     gwasglue2,
@@ -38,8 +37,6 @@ Suggests:
     testthat
 VignetteBuilder: 
     knitr
-Remotes:
-    mrcieu/gwasglue2
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1

R/query.R

@@ -240,42 +240,19 @@ batches <- function(access_token = check_access_token())
 #' Used to authenticate level of access to data. 
 #' By default, checks if already authenticated through [`get_access_token`] and 
 #' if not then does not perform authentication
-#' @param gwasglue Returns a gwasglue2 SummarySet object  (if `gwasglue = TRUE`).  Only one GWAS id can be queried at a time. See [gwasglue2::create_dataset()].Default = `FALSE`.
 #'
 #' @export
 #' @return Dataframe. If `gwasglue = TRUE` then returns a gwasglue2 object.
-associations <- function(variants, id, proxies=1, r2=0.8, align_alleles=1, palindromes=1, maf_threshold = 0.3, access_token=check_access_token(), gwasglue=FALSE){
+associations <- function(variants, id, proxies=1, r2=0.8, align_alleles=1, palindromes=1, maf_threshold = 0.3, access_token=check_access_token()){
 
 	# Query specific variants from specific GWAS using associations_query internal function (old version)
 	out <- associations_query(variants=variants, id=id, proxies=proxies, r2=r2, align_alleles=align_alleles, palindromes=palindromes, maf_threshold=maf_threshold, access_token=access_token)
-
-	if(gwasglue)
-	{
-		# check if it is a tibble (trying to avoid loading the tibble package)
-		if(inherits(out ,"tbl_df")){
-    		# output gwasglue2 SummarySet object
-			if(id %>% length() != 1){
-				stop("Only one GWAS ID can be queried at a time when using `gwasglue = TRUE`.")
-			} else {
-				# create gwasglue2 metadata 
-				m <- gwasglue2::create_metadata(gwasinfo(id))
-				# create gwasglue2 SummarySet object
-				s <- out %>% 
-					gwasglue2::create_summaryset(metadata=m, qc = TRUE) %>%
-					return()
-			}
-
-		} else {
-			return(out)
-		}
-	}
-	else{
-		return(out)
-	}
+
+	return(out)
 }
 
 
-# Query specific variants from specific GWAS - associations internal function to allow for gwasglue
+# Query specific variants from specific GWAS - associations internal function to allow for future gwasglue2 integration
 associations_query <- function(variants=variants, id=id, proxies=proxies, r2=r2, align_alleles=align_alleles, palindromes=palindromes, maf_threshold = maf_threshold, access_token=access_token)
 {
 	id <- legacy_ids(id)
@@ -396,42 +373,19 @@ phewas <- function(variants, pval = 0.00001, batch=c(), access_token=check_acces
 #' Used to authenticate level of access to data. 
 #' By default, checks if already authenticated through [`get_access_token`] 
 #' and if not then does not perform authentication.
-#' @param gwasglue Returns a gwasglue2 SummarySet object  (if `gwasglue = TRUE`).  Only one GWAS id can be queried at a time. See [gwasglue2::create_dataset()].Default = `FALSE`.
 #' @export
 #' @return Dataframe. If `gwasglue = TRUE` then returns a gwasglue2 object.
-tophits <- function(id, pval = 5e-8, clump = 1, r2 = 0.001, kb = 10000, pop="EUR", force_server = FALSE, access_token = check_access_token(), gwasglue = FALSE)
+tophits <- function(id, pval = 5e-8, clump = 1, r2 = 0.001, kb = 10000, pop="EUR", force_server = FALSE, access_token = check_access_token())
 {
 	# Query tophits from specific GWAS using tophits_query internal function (old version)
 	out <- tophits_query(id = id, pval = pval, clump = clump, r2 = r2, kb = kb, pop = pop, force_server = force_server, access_token = access_token)
 
-	if(isTRUE(gwasglue))
-	{
-		# check if it is a tibble (trying to avoid loading the tibble package)
-		if(inherits(out, "tbl_df")){
-    		# output gwasglue2 SummarySet object
-			if(id %>% length() != 1){
-				stop("Only one GWAS ID can be queried at a time when using `gwasglue = TRUE`.")
-			} else {
-				# create gwasglue2 metadata 
-				m <- gwasglue2::create_metadata(gwasinfo(id))
-				# create gwasglue2 SummarySet object
-				s <- out %>% 
-					gwasglue2::create_summaryset(metadata=m, qc = TRUE) %>%
-					return()
-			}
-
-		} else {
-			return(out)
-		}
-	}
-	else{
-		return(out)
-	}
+	return(out)
 }
 
 
 
-# query top hits from GWAS dataset - tophits internal function to allow for gwasglue
+# query top hits from GWAS dataset - tophits internal function to allow for future gwasglue2 integration
 tophits_query <- function(id, pval=5e-8, clump = 1, r2 = 0.001, kb = 10000, pop="EUR", 
                     force_server = FALSE, access_token=check_access_token())
 {