@@ -1,6 +1,6 @@

 Package: ISAnalytics

 Title: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

-Version: 1.3.7

+Version: 1.3.8

 Date: 2020-07-03

 Authors@R: c(

   person(given = "Andrea",

@@ -1110,8 +1110,8 @@ cumulative_count_union <- function(x,

 #' data("integration_matrices", package = "ISAnalytics")

 #' data("association_file", package = "ISAnalytics")

 #' aggreg <- aggregate_values_by_key(

-#'     x = rlang::current_env()$integration_matrices,

-#'     association_file = rlang::current_env()$association_file,

+#'     x = integration_matrices,

+#'     association_file = association_file,

 #'     value_cols = c("seqCount", "fragmentEstimate")

 #' )

 #' cumulated_is <- cumulative_is(aggreg)

@@ -1541,8 +1541,8 @@ is_sharing <- function(...,

 #' data("integration_matrices", package = "ISAnalytics")

 #' data("association_file", package = "ISAnalytics")

 #' aggreg <- aggregate_values_by_key(

-#'     x = rlang::current_env()$integration_matrices,

-#'     association_file = rlang::current_env()$association_file,

+#'     x = integration_matrices,

+#'     association_file = association_file,

 #'     value_cols = c("seqCount", "fragmentEstimate")

 #' )

 #' filtered_by_purity <- purity_filter(

@@ -1759,8 +1759,8 @@ purity_filter <- function(x,

 #' data("integration_matrices", package = "ISAnalytics")

 #' data("association_file", package = "ISAnalytics")

 #' aggreg <- aggregate_values_by_key(

-#'     x = rlang::current_env()$integration_matrices,

-#'     association_file = rlang::current_env()$association_file,

+#'     x = integration_matrices,

+#'     association_file = association_file,

 #'     value_cols = c("seqCount", "fragmentEstimate")

 #' )

 #' df1 <- aggreg %>%

@@ -1769,15 +1769,11 @@ purity_filter <- function(x,

 #'     dplyr::filter(.data$Tissue == "PB")

 #' source <- iss_source(df1, df2)

 #' source

-#' ggplot2::ggplot(source$PT001, ggplot2::aes(

-#'     x = as.factor(g2_TimePoint),

-#'     y = sharing_perc, fill = g1

-#' )) +

+#' ggplot2::ggplot(source$PT001, ggplot2::aes(x = as.factor(g2_TimePoint),

+#'                                            y = sharing_perc, fill = g1)) +

 #'     ggplot2::geom_col() +

-#'     ggplot2::labs(

-#'         x = "Time point", y = "Shared IS % with MNC BM",

-#'         title = "Source of is MNC BM vs MNC PB"

-#'     )

+#'     ggplot2::labs(x = "Time point", y = "Shared IS % with MNC BM",

+#'                   title = "Source of is MNC BM vs MNC PB")

 iss_source <- function(reference,

     selection,

     ref_group_key = c(

@@ -43,8 +43,8 @@ time point "t+1".

 data("integration_matrices", package = "ISAnalytics")

 data("association_file", package = "ISAnalytics")

 aggreg <- aggregate_values_by_key(

-    x = rlang::current_env()$integration_matrices,

-    association_file = rlang::current_env()$association_file,

+    x = integration_matrices,

+    association_file = association_file,

     value_cols = c("seqCount", "fragmentEstimate")

 )

 cumulated_is <- cumulative_is(aggreg)

@@ -52,8 +52,8 @@ observed for the first time.

 data("integration_matrices", package = "ISAnalytics")

 data("association_file", package = "ISAnalytics")

 aggreg <- aggregate_values_by_key(

-    x = rlang::current_env()$integration_matrices,

-    association_file = rlang::current_env()$association_file,

+    x = integration_matrices,

+    association_file = association_file,

     value_cols = c("seqCount", "fragmentEstimate")

 )

 df1 <- aggreg \%>\%

@@ -104,8 +104,8 @@ identified by the rows in the provided data frame are processed.

 data("integration_matrices", package = "ISAnalytics")

 data("association_file", package = "ISAnalytics")

 aggreg <- aggregate_values_by_key(

-    x = rlang::current_env()$integration_matrices,

-    association_file = rlang::current_env()$association_file,

+    x = integration_matrices,

+    association_file = association_file,

     value_cols = c("seqCount", "fragmentEstimate")

 )

 filtered_by_purity <- purity_filter(