round on function examples

R/classify.R

@@ -13,12 +13,12 @@
 #' the classification data and parameters.
 #' @export
 #' @examples
-#' # Example classification run on a single sample
 #' # First load example data
 #' data(MSK_genomic_data)
 #' data(MSK_clinical_data)
-#' # Initialize the INCOMMON object (note the outputs to screen)
-#' x = init(genomic_data = MSK_genomic_data[1:3,], clinical_data = MSK_clinical_data)
+#' # Initialize the INCOMMON object for a single sample (note the outputs to screen)
+#' sample = 'P-0002081'
+#' x = init(genomic_data = MSK_genomic_data %>% filter(sample == !!sample), clinical_data = MSK_clinical_data %>% filter(sample == !!sample))
 #' # Run INCOMMON classification
 #' x = classify(x = x, priors = pcawg_priors, entropy_cutoff = NULL, rho = 0.01)
 #' # An S3 method can be used to report to screen what is in the object

R/plot_classification.R

@@ -7,6 +7,17 @@
 #' a multi-faceted plot.
 #' @return An object or a list of objects of class \code{'ggplot2'}.
 #' @export
+#' @examples
+#' # First load example data
+#' data(MSK_genomic_data)
+#' data(MSK_clinical_data)
+#' # Initialize the INCOMMON object with a specific sample
+#' sample = 'P-0002081'
+#' x = init(genomic_data = MSK_genomic_data %>% filter(sample == !!sample), clinical_data = MSK_clinical_data %>% filter(sample == !!sample))
+#' # Run INCOMMON classification
+#' x = classify(x = x, priors = pcawg_priors, entropy_cutoff = NULL, rho = 0.01)
+#' # An S3 method can be used to report to screen what is in the object
+#' plot_classification(x = x, sample = sample)
 #' @importFrom dplyr filter mutate rename select %>%
 plot_classification = function(x, sample, assembly = F){