other small tweaks

R/createCellOffset.R

@@ -14,6 +14,7 @@
 #' @export
 #' @examples
 #' \dontrun{
+#' createCellOffset(expr.mat = sce_obj)
 #' createCellOffset(expr.mat = counts(sce_obj))
 #' createCellOffset(expr.mat = seu_obj, scale.factor = 1e5)
 #' }

R/summarizeModel.R

@@ -23,9 +23,11 @@ summarizeModel <- function(marge.model = NULL, pt = NULL) {
                      Slope.Segment = NA_real_,
                      Trend.Segment = NA_real_)
   } else {
-    # extract model equation & slopes
+    # extract model equation, slopes, & covariances
+    coef_vcov <- vcov(marge.model$final_mod)
     coef_df <- data.frame(coef_name = names(coef(marge.model$final_mod)),
-                          coef_value = unname(coef(marge.model$final_mod)))
+                          coef_value = unname(coef(marge.model$final_mod)),
+                          coef_var = unname(diag(coef_vcov)))
 
     coef_df <- coef_df[-which(coef_df$coef_name == "Intercept"), ]
 

inst/rmarkdown/templates/Bacher_Group_HTML/skeleton/skeleton.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "Title"
-subtitle: "University of Florida - Dept. of Biostatistics - Bacher Group"
+subtitle: "UF Dept. of Biostatistics - Bacher Group"
 author: "Name"
 date: "`r Sys.Date()`"
 output:
@@ -20,29 +20,40 @@ knitr::opts_chunk$set(echo = TRUE,
                       comment = NA, 
                       message = FALSE, 
                       warning = FALSE, 
-                      fig.align = "center")
+                      fig.align = "center", 
+                      dev = "png", 
+                      dpi = 300)
 set.seed(312)  # lucky seed
 ```
 
 # Libraries
 
 ```{r}
-library(glm2)
-library(mgcv)
 library(dplyr)
-library(scran)
 library(scLANE)
-library(scater)
 library(ggplot2)
-library(tradeSeq)
-library(slingshot)
-library(doParallel)
-library(kableExtra)
-library(SingleCellExperiment)
 ```
 
 # Data 
 
+```{r}
+
+```
+
 # Analysis 
 
+```{r}
+
+```
+
 # Conclusions 
+
+```{r}
+
+```
+
+# Session info 
+
+```{r}
+sessioninfo::session_info()
+```