Update IEU GWAS API

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MungeSumstats
 Type: Package
 Title: Standardise summary statistics from GWAS
-Version: 1.15.2
+Version: 1.15.3
 Authors@R:
     c(person(given = "Alan",
            family = "Murphy",
@@ -28,23 +28,20 @@ URL: https://github.com/neurogenomics/MungeSumstats
 BugReports: https://github.com/neurogenomics/MungeSumstats/issues
 License: Artistic-2.0
 Depends: R(>= 4.1)
-Imports: 
-    magrittr, 
+Imports:
     data.table,
     utils,
     R.utils,
     dplyr, 
     stats,
     GenomicRanges,
-    IRanges,
     GenomeInfoDb,
+    IRanges,
+    ieugwasr(>= 1.0.1),
     BSgenome,
     Biostrings,
     stringr,
     VariantAnnotation,
-    googleAuthR,
-    httr,
-    jsonlite,
     methods,
     parallel,
     rtracklayer(>= 1.59.1),

NAMESPACE

@@ -80,17 +80,7 @@ importFrom(dplyr,arrange)
 importFrom(dplyr,desc)
 importFrom(dplyr,mutate)
 importFrom(dplyr,rowwise)
-importFrom(dplyr,tibble)
-importFrom(googleAuthR,gar_auth)
-importFrom(httr,DELETE)
-importFrom(httr,GET)
-importFrom(httr,POST)
-importFrom(httr,add_headers)
-importFrom(httr,content)
-importFrom(httr,status_code)
-importFrom(httr,timeout)
-importFrom(jsonlite,fromJSON)
-importFrom(magrittr,"%>%")
+importFrom(ieugwasr,gwasinfo)
 importFrom(methods,is)
 importFrom(methods,show)
 importFrom(methods,slotNames)

NEWS.md

@@ -1,3 +1,15 @@
+## CHANGES IN VERSION 1.15.3
+
+### Bug fix
+*Updated retrieval of IEU OpenGWAS to new approach requiring login. Also updated
+to use the [IEU OpwnGWAS R package](https://github.com/MRCIEU/ieugwasr) as a 
+dependency.
+
+## CHANGES IN VERSION 1.15.2
+
+### New features
+*[FAQ Website](https://github.com/Al-Murphy/MungeSumstats/wiki/FAQ) updated.
+
 ## CHANGES IN VERSION 1.15.1
 
 ### New features

R/find_sumstats.R

@@ -39,23 +39,22 @@
 #' (e.g. \code{200000}).
 #' @param include_NAs Include datasets with missing metadata for size criteria
 #' (i.e. \code{min_sample_size}, \code{min_ncase}, or \code{min_ncontrol}).
-#' @inheritParams check_access_token
-#' @inheritParams gwasinfo 
-#' @inheritParams format_sumstats
 #' 
 #' @export
 #' @importFrom dplyr %>% arrange desc mutate rowwise
 #' @importFrom data.table setorderv
+#' @importFrom ieugwasr gwasinfo
 #' @examples
-#' # Only run the examples if user has internet access:
-#' if(try(is.character(getURL("www.google.com")))==TRUE){
+#' # Only run the examples if user has internet access
+#' # and if access token has been added
+#' if(try(is.character(getURL("www.google.com")))==TRUE && ieugwasr::get_opengwas_jwt()!=""){
 #' ### By ID
 #' metagwas <- find_sumstats(ids = c(
 #'     "ieu-b-4760",
 #'     "prot-a-1725",
 #'     "prot-a-664"
 #' ))
-#' ### By ID amd sample size
+#' ### By ID and sample size
 #' metagwas <- find_sumstats(
 #'     ids = c("ieu-b-4760", "prot-a-1725", "prot-a-664"),
 #'     min_sample_size = 5000
@@ -80,17 +79,16 @@ find_sumstats <- function(ids = NULL,
                           min_ncase = NULL,
                           min_ncontrol = NULL,
                           min_nsnp = NULL,
-                          include_NAs = FALSE,
-                          access_token = check_access_token()) {
+                          include_NAs = FALSE
+                          ) {
 
     ## Set up fake empty variables to avoid confusing BiocCheck
     sample_size <- ncase <- ncontrol <- nsnp <- N <- NULL;
 
     message("Collecting metadata from Open GWAS.")
     if (!is.null(ids)) {
-        metagwas <- gwasinfo(
-            id = ids,
-            access_token = access_token
+        metagwas <- ieugwasr::gwasinfo(
+            id = ids
         )
         ## gwasinfo() doesn't always return all columns for some reason
         missing_cols <- c("ncase", "ncontrol")
@@ -101,7 +99,7 @@ find_sumstats <- function(ids = NULL,
             }
         }
     } else {
-        metagwas <- gwasinfo()
+        metagwas <- ieugwasr::gwasinfo()
     }
     message("Filtering metadata by substring criteria.")
     if (!is.null(traits)) {