Commit ⋅ mrcieu/ieugwasr

Showing 1 of 7 files from the diff.

75.93% 66.67% -1.30%

R/query.R changed.

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tests/testthat/test_query.r has changed.

DESCRIPTION has changed.

vignettes/guide.Rmd has changed.

man/batches.Rd is new.

NAMESPACE has changed.

man/phewas.Rd has changed.

@@ -92,7 +92,12 @@

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{
	if(httr::status_code(response) >= 200 & httr::status_code(response) < 300)
	{
		return(jsonlite::fromJSON(httr::content(response, "text", encoding='UTF-8')))
		o <- jsonlite::fromJSON(httr::content(response, "text", encoding='UTF-8'))
		if('eaf' %in% names(o)) 
		{
			o[["eaf"]] <- as.numeric(o[["eaf"]])
		}
		return(o)
	} else {
		return(response)
		# stop("error code: ", httr::status_code(response), "\n  message: ", jsonlite::fromJSON(httr::content(response, "text", encoding='UTF-8')))

@@ -150,6 +155,24 @@

Loading

	dplyr::glimpse(x)
}

batch <- function(x) UseMethod("batch", x)
batch.GwasInfo <- function(x)
{
	sapply(strsplit(x[["id"]], "-"), function(x) paste(x[1], x[2], sep="-"))
}


#' Get list of data batches in IEU GWAS database
#'
#'
#' @param access_token Google OAuth2 access token. Used to authenticate level of access to data
#'
#' @export
#' @return data frame
batches <- function(access_token = check_access_token())
{
	api_query('batches', access_token=access_token) %>% get_query_content()
}

#' Query specific variants from specific GWAS
#'

@@ -196,15 +219,17 @@

Loading

#'
#' @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 access_token Google OAuth2 access token. Used to authenticate level of access to data. By default, checks if already authenticated through \code{get_access_token} and if not then does not perform authentication
#'
#' @export
#' @return Dataframe
phewas <- function(variants, pval = 0.00001, access_token=check_access_token())
phewas <- function(variants, pval = 0.00001, batch=c(), access_token=check_access_token())
{
	out <- api_query("phewas", query=list(
		variant=variants,
		pval=pval
		pval=pval,
		index_list=batch
	), access_token=access_token) %>% get_query_content()
	if(class(out) != "response")
	{

Files		•	•	•	Coverage
R	335	202	0	133	60.30%
Project Totals (7 files)	335	202	0	133	60.30%

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150	155		dplyr::glimpse(x)
151	156		}
152	157
	158	+	batch <- function(x) UseMethod("batch", x)
	159	+	batch.GwasInfo <- function(x)
	160	+	{
	161	+	sapply(strsplit(x[["id"]], "-"), function(x) paste(x[1], x[2], sep="-"))
	162	+	}
	163	+
	164	+
	165	+	#' Get list of data batches in IEU GWAS database
	166	+	#'
	167	+	#'
	168	+	#' @param access_token Google OAuth2 access token. Used to authenticate level of access to data
	169	+	#'
	170	+	#' @export
	171	+	#' @return data frame
	172	+	batches <- function(access_token = check_access_token())
	173	+	{
	174	+	api_query('batches', access_token=access_token) %>% get_query_content()
	175	+	}
153	176
154	177		#' Query specific variants from specific GWAS
155	178		#'

196	219		#'
197	220		#' @param variants Array of variants e.g. c("rs234", "7:105561135-105563135")
198	221		#' @param pval p-value threshold. Default = 0.00001
	222	+	#' @param batch Vector of batch IDs to search across. If c() (default) then returns all batches
199	223		#' @param access_token Google OAuth2 access token. Used to authenticate level of access to data. By default, checks if already authenticated through \code{get_access_token} and if not then does not perform authentication
200	224		#'
201	225		#' @export
202	226		#' @return Dataframe
203		-	phewas <- function(variants, pval = 0.00001, access_token=check_access_token())
	227	+	phewas <- function(variants, pval = 0.00001, batch=c(), access_token=check_access_token())
204	228		{
205	229		out <- api_query("phewas", query=list(
206	230		variant=variants,
207		-	pval=pval
	231	+	pval=pval,
	232	+	index_list=batch
208	233		), access_token=access_token) %>% get_query_content()
209	234		if(class(out) != "response")
210	235		{

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92	92		{
93	93		if(httr::status_code(response) >= 200 & httr::status_code(response) < 300)
94	94		{
95		-	return(jsonlite::fromJSON(httr::content(response, "text", encoding='UTF-8')))
	95	+	o <- jsonlite::fromJSON(httr::content(response, "text", encoding='UTF-8'))
	96	+	if('eaf' %in% names(o))
	97	+	{
	98	+	o[["eaf"]] <- as.numeric(o[["eaf"]])
	99	+	}
	100	+	return(o)
96	101		} else {
97	102		return(response)
98	103		# stop("error code: ", httr::status_code(response), "\n message: ", jsonlite::fromJSON(httr::content(response, "text", encoding='UTF-8')))

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