Merge pull request #144 from MRCIEU/devel

Various updates

Author: explodecomputer

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ieugwasr
 Title: Interface to the 'OpenGWAS' Database API
-Version: 1.0.4
+Version: 1.1.0
 Authors@R: c(
     person("Gibran", "Hemani", , "g.hemani@bristol.ac.uk", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0003-0920-1055")),

R/afl2.r

@@ -8,14 +8,15 @@
 #' @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 ... Additional arguments passed to `api_query()`.
 #'
 #' @export
 #' @return Data frame containing ancestry specific LD scores and allele frequencies for each variant
-afl2_list <- function(variantlist="reduced", opengwas_jwt=get_opengwas_jwt())
+afl2_list <- function(variantlist="reduced", opengwas_jwt=get_opengwas_jwt(), ...)
 {
 	if(variantlist == "reduced")
 	{
-		api_query("variants/afl2/snplist", opengwas_jwt=opengwas_jwt) %>% 
+		api_query("variants/afl2/snplist", opengwas_jwt=opengwas_jwt, ...) %>% 
 			get_query_content() %>%
 			dplyr::as_tibble() %>%
 			return()
@@ -35,12 +36,13 @@ afl2_list <- function(variantlist="reduced", opengwas_jwt=get_opengwas_jwt())
 #' @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 ... Additional arguments passed to `api_query()`.
 #'
 #' @export
 #' @return Data frame containing ancestry specific LD scores and allele frequencies for each variant
-afl2_rsid <- function(rsid, reference="1000g", opengwas_jwt=get_opengwas_jwt())
+afl2_rsid <- function(rsid, reference="1000g", opengwas_jwt=get_opengwas_jwt(), ...)
 {
-	out <- api_query("variants/afl2", list(rsid=rsid), opengwas_jwt=opengwas_jwt) %>% get_query_content()
+	out <- api_query("variants/afl2", list(rsid=rsid), opengwas_jwt=opengwas_jwt, ...) %>% get_query_content()
 	if(inherits(out, "response"))
 	{
 		return(out)
@@ -57,12 +59,13 @@ afl2_rsid <- function(rsid, reference="1000g", opengwas_jwt=get_opengwas_jwt())
 #' 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 ... Additional arguments passed to `api_query()`.
 #'
 #' @export
 #' @return Data frame containing ancestry specific LD scores and allele frequencies for each variant
-afl2_chrpos <- function(chrpos, reference="1000g", opengwas_jwt=get_opengwas_jwt())
+afl2_chrpos <- function(chrpos, reference="1000g", opengwas_jwt=get_opengwas_jwt(), ...)
 {
-	out <- api_query("variants/afl2", list(chrpos=chrpos), opengwas_jwt=opengwas_jwt) %>% get_query_content()
+	out <- api_query("variants/afl2", list(chrpos=chrpos), opengwas_jwt=opengwas_jwt, ...) %>% get_query_content()
 	if(inherits(out, "response"))
 	{
 		return(out)
@@ -83,14 +86,15 @@ afl2_chrpos <- function(chrpos, reference="1000g", opengwas_jwt=get_opengwas_jwt
 #' @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 ... Additional arguments passed to `afl2_list()`
 #'
 #' @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
-infer_ancestry <- function(d, snpinfo=NULL, opengwas_jwt=get_opengwas_jwt())
+infer_ancestry <- function(d, snpinfo=NULL, opengwas_jwt=get_opengwas_jwt(), ...)
 {
 	if(is.null(snpinfo))
 	{
-		snpinfo <- afl2_list(opengwas_jwt=opengwas_jwt)
+		snpinfo <- afl2_list(opengwas_jwt=opengwas_jwt, ...)
 	}
 	snpinfo <- snpinfo %>%
 		dplyr::inner_join(., d, by="rsid")

R/ld_clump.R

@@ -31,12 +31,13 @@
 #' @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`
+#' Default = `NULL`,
+#' @param ... Additional arguments passed to `ld_clump_local()`.
 #'
 #' @export
 #' @return Data frame
 ld_clump <- function(dat=NULL, clump_kb=10000, clump_r2=0.001, clump_p=0.99, 
-                     pop = "EUR", opengwas_jwt=get_opengwas_jwt(), bfile=NULL, plink_bin=NULL)
+                     pop = "EUR", opengwas_jwt=get_opengwas_jwt(), bfile=NULL, plink_bin=NULL, ...)
 {
 
 	stopifnot("rsid" %in% names(dat))
@@ -84,7 +85,7 @@ ld_clump <- function(dat=NULL, clump_kb=10000, clump_r2=0.001, clump_p=0.99,
 			if(is.null(bfile))
 			{
 			  message("Clumping ", ids[i], ", ", nrow(x), " variants, using ", pop, " population reference")
-			  res[[i]] <- ld_clump_api(x, clump_kb=clump_kb, clump_r2=clump_r2, clump_p=clump_p, pop=pop, opengwas_jwt=opengwas_jwt)
+			  res[[i]] <- ld_clump_api(x, clump_kb=clump_kb, clump_r2=clump_r2, clump_p=clump_p, pop=pop, opengwas_jwt=opengwas_jwt, ...)
 			} else {
 			  message("Clumping ", ids[i], ", ", nrow(x), " variants, using: ", bfile)
 				res[[i]] <- ld_clump_local(x, clump_kb=clump_kb, clump_r2=clump_r2, clump_p=clump_p, bfile=bfile, plink_bin=plink_bin)
@@ -106,8 +107,9 @@ ld_clump <- function(dat=NULL, clump_kb=10000, clump_r2=0.001, clump_p=0.99,
 #' @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 ... Additional arguments passed to `api_query()`.
 #' @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())
+ld_clump_api <- function(dat, clump_kb=10000, clump_r2=0.1, clump_p, pop="EUR", opengwas_jwt=get_opengwas_jwt(), ...)
 {
 	res <- api_query('ld/clump',
 			query = list(
@@ -118,7 +120,7 @@ ld_clump_api <- function(dat, clump_kb=10000, clump_r2=0.1, clump_p, pop="EUR",
 				kb = clump_kb,
 				pop = pop
 			),
-			opengwas_jwt=opengwas_jwt
+			opengwas_jwt=opengwas_jwt, ...
 		) %>% get_query_content()
 	y <- subset(dat, !dat[["rsid"]] %in% res)
 	if(nrow(y) > 0)
@@ -195,17 +197,18 @@ random_string <- function(n=1, len=6)
 #' @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 ... Additional arguments passed to `api_query()`.
 #'
 #' @export
 #' @return Array of rsids that are present in the LD reference panel
-ld_reflookup <- function(rsid, pop='EUR', opengwas_jwt=get_opengwas_jwt())
+ld_reflookup <- function(rsid, pop='EUR', opengwas_jwt=get_opengwas_jwt(), ...)
 {
 	res <- api_query('ld/reflookup',
 			query = list(
 				rsid = rsid,
 				pop = pop
 			),
-			opengwas_jwt=opengwas_jwt
+			opengwas_jwt=opengwas_jwt, ...
 		) %>% get_query_content()
 	if(length(res) == 0)
 	{

R/ld_matrix.R

@@ -30,10 +30,11 @@
 #' @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`
+#' @param ... Additional arguments passed to `ld_matrix_api()`.
 #'
 #' @export
 #' @return Matrix of LD r values
-ld_matrix <- function(variants, with_alleles=TRUE, pop="EUR", opengwas_jwt=get_opengwas_jwt(), bfile=NULL, plink_bin=NULL) {
+ld_matrix <- function(variants, with_alleles=TRUE, pop="EUR", opengwas_jwt=get_opengwas_jwt(), bfile=NULL, plink_bin=NULL, ...) {
 	if(length(variants) > 500 & is.null(bfile))
 	{
 		stop("SNP list must be smaller than 500. Try running locally by providing local ld reference with bfile argument. See vignettes for a guide on how to do this.")
@@ -56,7 +57,7 @@ ld_matrix <- function(variants, with_alleles=TRUE, pop="EUR", opengwas_jwt=get_o
 		return(ld_matrix_local(variants, bfile=bfile, plink_bin=plink_bin, with_alleles=with_alleles))
 	}
 
-	res <- api_query('ld/matrix', query = list(rsid=variants, pop=pop), opengwas_jwt=opengwas_jwt) %>% get_query_content()
+	res <- api_query('ld/matrix', query = list(rsid=variants, pop=pop), opengwas_jwt=opengwas_jwt, ...) %>% get_query_content()
 
 	if(all(is.na(res))) stop("None of the requested variants were found")
 	variants2 <- res$snplist