@@ -1,7 +1,7 @@

 Package: COMPASS

 Type: Package

 Title: Combinatorial Polyfunctionality Analysis of Single Cells

-Version: 1.29.0

+Version: 1.29.1

 Date: 2014-07-11

 Author: Lynn Lin, Kevin Ushey, Greg Finak, Ravio Kolde (pheatmap)

 Authors@R: c( person("Lynn", "Lin", role="aut", email="[email protected]"),

@@ -17,6 +17,7 @@

 ##' @param replications The number of 'replications' to perform. In order to

 ##'   conserve memory, we only keep the model estimates from the last replication.

 ##' @param verbose Boolean; if \code{TRUE} we output progress information.

+##' @param seed A seed for the random number generator. Defaults to 100.

 ##' @return A \code{list} with class \code{COMPASSResult} with two components,

 ##'   the \code{fit} containing parameter estimates and parameter acceptance

 ##'   rates, and \code{data} containing the generated data used as input for

@@ -52,7 +53,7 @@

 ##' ## prefer using more iterations for a real fit

 ##' scr = SimpleCOMPASS(n_s, n_u, meta, "iid", iterations=1000)

 SimpleCOMPASS <- function(n_s, n_u, meta, individual_id,

-  iterations=1E4, replications=8, verbose=TRUE) {

+  iterations=1E4, replications=8, verbose=TRUE,seed=100) {

   # Order, n_s, n_u, and meta (if needed)

@@ -67,7 +68,8 @@ SimpleCOMPASS <- function(n_s, n_u, meta, individual_id,

   message("Ordering meta, n_s and n_u by individual_id since this wasn't done.\n",

           "If you think this is an error, check your data and rerun the code.")

   }

-  set.seed(100);

+  cat("Setting the seed to ",seed,"\n");

+  set.seed(seed)

   if (!all(colnames(n_s) == colnames(n_u))) {

     stop("The column names of 'n_s' and 'n_u' do not match.")

   }