... | ... |
@@ -1110,8 +1110,8 @@ cumulative_count_union <- function(x, |
1110 | 1110 |
#' data("integration_matrices", package = "ISAnalytics") |
1111 | 1111 |
#' data("association_file", package = "ISAnalytics") |
1112 | 1112 |
#' aggreg <- aggregate_values_by_key( |
1113 |
-#' x = rlang::current_env()$integration_matrices, |
|
1114 |
-#' association_file = rlang::current_env()$association_file, |
|
1113 |
+#' x = integration_matrices, |
|
1114 |
+#' association_file = association_file, |
|
1115 | 1115 |
#' value_cols = c("seqCount", "fragmentEstimate") |
1116 | 1116 |
#' ) |
1117 | 1117 |
#' cumulated_is <- cumulative_is(aggreg) |
... | ... |
@@ -1541,8 +1541,8 @@ is_sharing <- function(..., |
1541 | 1541 |
#' data("integration_matrices", package = "ISAnalytics") |
1542 | 1542 |
#' data("association_file", package = "ISAnalytics") |
1543 | 1543 |
#' aggreg <- aggregate_values_by_key( |
1544 |
-#' x = rlang::current_env()$integration_matrices, |
|
1545 |
-#' association_file = rlang::current_env()$association_file, |
|
1544 |
+#' x = integration_matrices, |
|
1545 |
+#' association_file = association_file, |
|
1546 | 1546 |
#' value_cols = c("seqCount", "fragmentEstimate") |
1547 | 1547 |
#' ) |
1548 | 1548 |
#' filtered_by_purity <- purity_filter( |
... | ... |
@@ -1759,8 +1759,8 @@ purity_filter <- function(x, |
1759 | 1759 |
#' data("integration_matrices", package = "ISAnalytics") |
1760 | 1760 |
#' data("association_file", package = "ISAnalytics") |
1761 | 1761 |
#' aggreg <- aggregate_values_by_key( |
1762 |
-#' x = rlang::current_env()$integration_matrices, |
|
1763 |
-#' association_file = rlang::current_env()$association_file, |
|
1762 |
+#' x = integration_matrices, |
|
1763 |
+#' association_file = association_file, |
|
1764 | 1764 |
#' value_cols = c("seqCount", "fragmentEstimate") |
1765 | 1765 |
#' ) |
1766 | 1766 |
#' df1 <- aggreg %>% |
... | ... |
@@ -1769,15 +1769,11 @@ purity_filter <- function(x, |
1769 | 1769 |
#' dplyr::filter(.data$Tissue == "PB") |
1770 | 1770 |
#' source <- iss_source(df1, df2) |
1771 | 1771 |
#' source |
1772 |
-#' ggplot2::ggplot(source$PT001, ggplot2::aes( |
|
1773 |
-#' x = as.factor(g2_TimePoint), |
|
1774 |
-#' y = sharing_perc, fill = g1 |
|
1775 |
-#' )) + |
|
1772 |
+#' ggplot2::ggplot(source$PT001, ggplot2::aes(x = as.factor(g2_TimePoint), |
|
1773 |
+#' y = sharing_perc, fill = g1)) + |
|
1776 | 1774 |
#' ggplot2::geom_col() + |
1777 |
-#' ggplot2::labs( |
|
1778 |
-#' x = "Time point", y = "Shared IS % with MNC BM", |
|
1779 |
-#' title = "Source of is MNC BM vs MNC PB" |
|
1780 |
-#' ) |
|
1775 |
+#' ggplot2::labs(x = "Time point", y = "Shared IS % with MNC BM", |
|
1776 |
+#' title = "Source of is MNC BM vs MNC PB") |
|
1781 | 1777 |
iss_source <- function(reference, |
1782 | 1778 |
selection, |
1783 | 1779 |
ref_group_key = c( |
... | ... |
@@ -43,8 +43,8 @@ time point "t+1". |
43 | 43 |
data("integration_matrices", package = "ISAnalytics") |
44 | 44 |
data("association_file", package = "ISAnalytics") |
45 | 45 |
aggreg <- aggregate_values_by_key( |
46 |
- x = rlang::current_env()$integration_matrices, |
|
47 |
- association_file = rlang::current_env()$association_file, |
|
46 |
+ x = integration_matrices, |
|
47 |
+ association_file = association_file, |
|
48 | 48 |
value_cols = c("seqCount", "fragmentEstimate") |
49 | 49 |
) |
50 | 50 |
cumulated_is <- cumulative_is(aggreg) |
... | ... |
@@ -52,8 +52,8 @@ observed for the first time. |
52 | 52 |
data("integration_matrices", package = "ISAnalytics") |
53 | 53 |
data("association_file", package = "ISAnalytics") |
54 | 54 |
aggreg <- aggregate_values_by_key( |
55 |
- x = rlang::current_env()$integration_matrices, |
|
56 |
- association_file = rlang::current_env()$association_file, |
|
55 |
+ x = integration_matrices, |
|
56 |
+ association_file = association_file, |
|
57 | 57 |
value_cols = c("seqCount", "fragmentEstimate") |
58 | 58 |
) |
59 | 59 |
df1 <- aggreg \%>\% |
... | ... |
@@ -104,8 +104,8 @@ identified by the rows in the provided data frame are processed. |
104 | 104 |
data("integration_matrices", package = "ISAnalytics") |
105 | 105 |
data("association_file", package = "ISAnalytics") |
106 | 106 |
aggreg <- aggregate_values_by_key( |
107 |
- x = rlang::current_env()$integration_matrices, |
|
108 |
- association_file = rlang::current_env()$association_file, |
|
107 |
+ x = integration_matrices, |
|
108 |
+ association_file = association_file, |
|
109 | 109 |
value_cols = c("seqCount", "fragmentEstimate") |
110 | 110 |
) |
111 | 111 |
filtered_by_purity <- purity_filter( |