saving time on the examples by avoiding unnecessary full run of `DESe…

…q()` if not strictly necessary
imbeimainz · Apr 22, 2024 · 494d6bc · 494d6bc
1 parent 0f0e553
commit 494d6bc
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Showing 5 changed files with 6 additions and 6 deletions.
diff --git a/R/gene_plot.R b/R/gene_plot.R
@@ -58,7 +58,7 @@
 #' rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
 #' keep <- rowSums(counts(dds_macrophage) >= 10) >= 6
 #' dds_macrophage <- dds_macrophage[keep, ]
-#' dds_macrophage <- DESeq(dds_macrophage)
+#' # dds_macrophage <- DESeq(dds_macrophage)
 #'
 #' # annotation object
 #' anno_df <- data.frame(
@@ -249,7 +249,7 @@ gene_plot <- function(de_container,
 #' rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
 #' keep <- rowSums(counts(dds_macrophage) >= 10) >= 6
 #' dds_macrophage <- dds_macrophage[keep, ]
-#' dds_macrophage <- DESeq(dds_macrophage)
+#' # dds_macrophage <- DESeq(dds_macrophage)
 #'
 #' df_exp <- get_expr_values(
 #'   de_container = dds_macrophage,

diff --git a/R/mosdef_check_inputs.R b/R/mosdef_check_inputs.R
@@ -81,7 +81,7 @@ mosdef_res_check <- function(res_de,
 #' rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
 #' keep <- rowSums(counts(dds_macrophage) >= 10) >= 6
 #' dds_macrophage <- dds_macrophage[keep, ]
-#' dds_macrophage <- DESeq(dds_macrophage)
+#' # dds_macrophage <- DESeq(dds_macrophage)
 #'
 #' mosdef_de_container_check(dds_macrophage)
 mosdef_de_container_check <- function(de_container,

diff --git a/man/gene_plot.Rd b/man/gene_plot.Rd
diff --git a/man/get_expr_values.Rd b/man/get_expr_values.Rd
diff --git a/man/mosdef_de_container_check.Rd b/man/mosdef_de_container_check.Rd