Convert api.opengwas.io text into a URL in docs

R/afl2.r

@@ -7,7 +7,7 @@
 #'
 #' @param variantlist Choose pre-defined list. reduced = ~20k SNPs that are 
 #' common in all super populations (default). hapmap3 = ~1.3 million hm3 SNPs
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return Data frame containing ancestry specific LD scores and allele frequencies for each variant
@@ -34,7 +34,7 @@ afl2_list <- function(variantlist=c("reduced", "hapmap3")[1], opengwas_jwt=get_o
 #'
 #' @param rsid Vector of rsids
 #' @param reference Default=`"1000g"`
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return Data frame containing ancestry specific LD scores and allele frequencies for each variant
@@ -56,7 +56,7 @@ afl2_rsid <- function(rsid, reference="1000g", opengwas_jwt=get_opengwas_jwt())
 #' @param chrpos list of `<chr>:<pos>` in build 37, e.g. `c("3:46414943", "3:122991235")`. 
 #' Also allows ranges e.g `"7:105561135-105563135"`
 #' @param reference Default=`"1000g"`
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return Data frame containing ancestry specific LD scores and allele frequencies for each variant
@@ -82,7 +82,7 @@ afl2_chrpos <- function(chrpos, reference="1000g", opengwas_jwt=get_opengwas_jwt
 #' e.g. output from associations
 #' @param snpinfo Output from [`afl2_list`], [`afl2_rsid`] or [`afl2_chrpos`]. 
 #' If `NULL` then [`afl2_list()`] is used by default
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return data frame ordered by most likely ancestry, each row represents a super population and cor column represents the correlation between the GWAS dataset and the 1000 genomes super population allele frequencies

R/api.R

@@ -40,7 +40,7 @@ get_opengwas_jwt <- function() {
 
 #' Get user details
 #' 
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #' 
 #' @export
 #' @return user information

R/ld_clump.R

@@ -27,7 +27,7 @@
 #' Options are `"EUR"`, `"SAS"`, `"EAS"`, `"AFR"`, `"AMR"`. 
 #' `'legacy'` also available - which is a previously used verison of the EUR 
 #' panel with a slightly different set of markers
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.#' 
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.#' 
 #' @param bfile If this is provided then will use the API. Default = `NULL`
 #' @param plink_bin If `NULL` and `bfile` is not `NULL` then will detect 
 #' packaged plink binary for specific OS. Otherwise specify path to plink binary. 
@@ -97,7 +97,7 @@ ld_clump <- function(dat=NULL, clump_kb=10000, clump_r2=0.001, clump_p=0.99,
 #' @param clump_p Clumping sig level for index variants. Default = `1` (i.e. no threshold)
 #' @param pop Super-population to use as reference panel. Default = `"EUR"`. 
 #' Options are `"EUR"`, `"SAS"`, `"EAS"`, `"AFR"`, `"AMR"`
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.#' @param bfile If this is provided then will use the API. Default = `NULL`
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.#' @param bfile If this is provided then will use the API. Default = `NULL`
 #' @return Data frame of only independent variants
 ld_clump_api <- function(dat, clump_kb=10000, clump_r2=0.1, clump_p, pop="EUR", opengwas_jwt=get_opengwas_jwt())
 {
@@ -186,7 +186,7 @@ random_string <- function(n=1, len=6)
 #' @param rsid Array of rsids to check
 #' @param pop Super-population to use as reference panel. Default = `"EUR"`. 
 #' Options are `"EUR"`, `"SAS"`, `"EAS"`, `"AFR"`, `"AMR"`
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.#' @param bfile If this is provided then will use the API. Default = `NULL`
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.#' @param bfile If this is provided then will use the API. Default = `NULL`
 #'
 #' @export
 #' @return Array of rsids that are present in the LD reference panel

R/ld_matrix.R

@@ -26,7 +26,7 @@
 #' Options are `"EUR"`, `"SAS"`, `"EAS"`, `"AFR"`, `"AMR"`. 
 #' `'legacy'` also available - which is a previously used verison of the EUR 
 #' panel with a slightly different set of markers
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.#' @param bfile If this is provided then will use the API. Default = `NULL`
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.#' @param bfile If this is provided then will use the API. Default = `NULL`
 #' @param bfile If this is provided then will use the API. Default = `NULL`
 #' @param plink_bin If `NULL` and bfile is not `NULL` then will detect packaged 
 #' plink binary for specific OS. Otherwise specify path to plink binary. Default = `NULL`

R/query.R

@@ -5,7 +5,7 @@
 #'
 #' @param path Either a full query path (e.g. for get) or an endpoint (e.g. for post) queries
 #' @param query If post query, provide a list of arguments as the payload. `NULL` by default
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #' @param method `"GET"` (default) or `"POST"`, `"DELETE"` etc
 #' @param silent `TRUE`/`FALSE` to be passed to httr call. `TRUE` by default
 #' @param encode Default = `"json"`, see [`httr::POST`] for options
@@ -166,7 +166,7 @@ print.ApiStatus <- function(x, ...)
 #'
 #' @param id List of MR-Base IDs to retrieve. If `NULL` (default) retrieves all 
 #' available datasets
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return Dataframe of details for all available studies
@@ -213,7 +213,7 @@ batch_from_id <- function(id)
 
 #' Get list of data batches in IEU GWAS database
 #'
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return data frame
@@ -240,7 +240,7 @@ batches <- function(opengwas_jwt=get_opengwas_jwt())
 #' `1` = yes (default), `0` = no
 #' @param palindromes Allow palindromic SNPs (if `proxies = 1`). `1` = yes (default), `0` = no
 #' @param maf_threshold MAF threshold to try to infer palindromic SNPs. Default = `0.3`.
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return Dataframe
@@ -271,7 +271,7 @@ associations <- function(variants, id, proxies=1, r2=0.8, align_alleles=1, palin
 #' Look up sample sizes when meta data is missing from associations
 #'
 #' @param d Output from [`associations`]
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return Updated version of d
@@ -315,7 +315,7 @@ fix_n <- function(d)
 #' @param variants Array of variants e.g. `c("rs234", "7:105561135-105563135")`
 #' @param pval p-value threshold. Default = `0.00001`
 #' @param batch Vector of batch IDs to search across. If `c()` (default) then returns all batches
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return Dataframe
@@ -357,7 +357,7 @@ phewas <- function(variants, pval = 0.00001, batch=c(), opengwas_jwt=get_opengwa
 #' If force_server = `TRUE` then will recompute using server side LD reference panel.
 #' @param pop Super-population to use as reference panel. Default = `"EUR"`. 
 #' Options are `"EUR"`, `"SAS"`, `"EAS"`, `"AFR"`, `"AMR"`
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return Dataframe
@@ -399,7 +399,7 @@ tophits <- function(id, pval=5e-8, clump = 1, r2 = 0.001, kb = 10000, pop="EUR",
 #' Check datasets that are in process of being uploaded
 #'
 #' @param id ID
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return Dataframe

R/variants.R

@@ -5,7 +5,7 @@
 #' @param gene Vector of genes, either Ensembl or Entrez, 
 #' e.g. `c("ENSG00000123374", "ENSG00000160791")` or `1017`
 #' @param radius Radius around the gene region to include. Default = `0`
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return data frame with the following columns
@@ -30,7 +30,7 @@ variants_gene <- function(gene, radius=0, opengwas_jwt=get_opengwas_jwt())
 #'
 #'
 #' @param rsid Vector of rsids
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return data frame
@@ -57,7 +57,7 @@ variants_rsid <- function(rsid, opengwas_jwt=get_opengwas_jwt())
 #' @param chrpos list of `<chr>:<pos>` in build 37, 
 #' e.g. `c("3:46414943", "3:122991235")`. Also allows ranges e.g. `"7:105561135-105563135"`
 #' @param radius Radius around each chrpos, default = `0`
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return Data frame
@@ -78,7 +78,7 @@ variants_chrpos <- function(chrpos, radius=0, opengwas_jwt=get_opengwas_jwt())
 #' Convert mixed array of rsid and chrpos to list of rsid
 #'
 #' @param variants Array of variants e.g. `c("rs234", "7:105561135-105563135")`
-#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return list of rsids