updates

NAMESPACE

@@ -37,7 +37,6 @@ export(get_population_allele_frequency)
 export(get_r_from_lor)
 export(get_r_from_pn)
 export(harmonise_data)
-export(ios)
 export(ld_matrix)
 export(make_dat)
 export(mr)

R/add_metadata.r

@@ -20,17 +20,17 @@ add_metadata <- function(dat, cols = c("sample_size", "ncase", "ncontrol", "unit
 			message(what, ": none of the IDs found in database")
 			return(NULL)
 		}
-
 		for(col in cols)
 		{
 			if(!col %in% names(info))
 			{
 				info[[col]] <- NA
 			}
 		}
-
-		info <- dplyr::select(info, "id", "sample_size", "ncase", "ncontrol", "unit", "sd")
-		names(info) <- paste0(names(info), ".", what)		
+		info <- subset(info, select=c("id", cols))
+		names(info) <- paste0(names(info), ".", what)
+		index <- grepl("ukb-d", info$id) & is.na(info$sample_size)
+		info$sample_size[index] <- 300000
 		return(info)
 	}
 
@@ -61,5 +61,6 @@ add_metadata <- function(dat, cols = c("sample_size", "ncase", "ncontrol", "unit
 
 	dat <- dat[dat[[order_col]], ]
 	dat <- dat[, !names(dat) %in% order_col]
+	# dat <- fix_ukb_d(dat)
 	return(dat)
 }

tests/testthat/test_add_metadata.r

@@ -41,3 +41,9 @@ test_that("no id2", {
 	d <- add_metadata(d)
 	expect_true(!"units.outcome" %in% names(d))
 })
+
+test_that("ukb-d", {
+	d <- extract_outcome_data(exposure$SNP, 'ukb-d-30710_irnt')
+	d <- add_metadata(d)
+	expect_true("units.outcome" %in% names(d))
+}

tests/testthat/test_rsq.r

@@ -28,3 +28,8 @@ test_that("dat 2", {
 	expect_true("rsq.outcome" %in% names(d) & "rsq.exposure" %in% names(d))
 })
 
+test_that("dat ukb-d", {
+	d <- make_dat(exposure="ukb-d-30710_irnt", proxies=FALSE) %>% add_rsq()
+	expect_true("rsq.outcome" %in% names(d) & "rsq.exposure" %in% names(d))
+})
+