More DOI replacements

R/integration.R

@@ -92,7 +92,7 @@ NULL
 #' \code{\link{IntegrateData}}.
 #'
 #' @references Stuart T, Butler A, et al. Comprehensive Integration of
-#' Single-Cell Data. Cell. 2019;177:1888-1902 \url{https://doi.org/10.1016/j.cell.2019.05.031}
+#' Single-Cell Data. Cell. 2019;177:1888-1902 \doi{10.1016/j.cell.2019.05.031}
 #'
 #' @importFrom pbapply pblapply
 #' @importFrom future.apply future_lapply
@@ -535,7 +535,7 @@ FindIntegrationAnchors <- function(
 #' \code{\link{TransferData}}
 #'
 #' @references Stuart T, Butler A, et al. Comprehensive Integration of
-#' Single-Cell Data. Cell. 2019;177:1888-1902 \url{https://doi.org/10.1016/j.cell.2019.05.031};
+#' Single-Cell Data. Cell. 2019;177:1888-1902 \doi{10.1016/j.cell.2019.05.031};
 #'
 #' @export
 #' @concept integration
@@ -905,8 +905,7 @@ GetTransferPredictions <- function(object, assay = "predictions", slot = "data",
 #'
 #' The main steps of this procedure are outlined below. For a more detailed
 #' description of the methodology, please see Stuart, Butler, et al Cell 2019.
-#' \url{https://doi.org/10.1016/j.cell.2019.05.031};
-#' \url{https://doi.org/10.1101/460147}
+#' \doi{10.1016/j.cell.2019.05.031}; \doi{10.1101/460147}
 #'
 #' For pairwise integration:
 #'
@@ -983,7 +982,7 @@ GetTransferPredictions <- function(object, assay = "predictions", slot = "data",
 #' as centered, corrected Pearson residuals.
 #'
 #' @references Stuart T, Butler A, et al. Comprehensive Integration of
-#' Single-Cell Data. Cell. 2019;177:1888-1902 \url{https://doi.org/10.1016/j.cell.2019.05.031}
+#' Single-Cell Data. Cell. 2019;177:1888-1902 \doi{10.1016/j.cell.2019.05.031}
 #'
 #' @export
 #' @concept integration
@@ -2410,7 +2409,7 @@ SelectIntegrationFeatures <- function(
 #'
 #'
 #' @references Stuart T, Butler A, et al. Comprehensive Integration of
-#' Single-Cell Data. Cell. 2019;177:1888-1902 \url{https://doi.org/10.1016/j.cell.2019.05.031}
+#' Single-Cell Data. Cell. 2019;177:1888-1902 \doi{10.1016/j.cell.2019.05.031}
 #'
 #' @export
 #' @concept integration