@@ -77,15 +77,18 @@ exportMethods(perplexity)

 exportMethods(resList)

 exportMethods(runParams)

 exportMethods(sampleLabel)

+import(MAST, except = c(combine))

 import(RColorBrewer)

 import(Rcpp)

 import(RcppEigen)

+import(SummarizedExperiment, except = c(shift, rowRanges))

 import(data.table)

 import(foreach)

 import(grDevices)

 import(graphics)

 import(grid)

 import(gridExtra)

+import(gridExtra, except = c(combine))

 import(gtable)

 import(matrixStats, except = c(count))

 import(plyr)

@@ -24,6 +24,7 @@

 #' celda.mod = celda_C(celda.C.sim$counts, K=celda.C.sim$K, 

 #'                     sample.label=celda.C.sim$sample.label)

 #' @import Rcpp RcppEigen

+#' @rawNamespace import(gridExtra, except = c(combine))

 #' @export

 celda_C = function(counts, sample.label=NULL, K, alpha=1, beta=1,

   					        algorithm = c("EM", "Gibbs"), 

@@ -30,6 +30,7 @@

 #' celda.mod = celda_CG(celda.CG.sim$counts, K=celda.CG.sim$K, L=celda.CG.sim$L,

 #'                      sample.label=celda.CG.sim$sample.label, nchains=1)

 #' @import Rcpp RcppEigen

+#' @rawNamespace import(gridExtra, except = c(combine))

 #' @export

 celda_CG = function(counts, sample.label=NULL, K, L,

                     alpha=1, beta=1, delta=1, gamma=1, 

@@ -12,8 +12,9 @@

 #' @examples

 #' cluster.diffexp.res = differentialExpression(celda.CG.sim$counts, celda.CG.mod, c1=c(1,2))

 #' @export

-#' @import data.table

-#' @import plyr

+#' @import data.table plyr

+#' @rawNamespace import(MAST, except = c(combine))

+#' @rawNamespace import(SummarizedExperiment, except = c(shift, rowRanges))

 differentialExpression <- function(counts, celda.mod, c1, c2 = NULL, only.pos = FALSE, log2fc.threshold = NULL, fdr.threshold = 1) {

   if (!is.matrix(counts)) {

     stop("'counts' should be a numeric count matrix")

old mode 100755

new mode 100644