@@ -8,6 +8,4 @@ inst/doc

 # R CMD build/check outputs

 *.Rcheck

 FuseSOM*.tar.gz

-

-# debugging code

-debug.R 

\ No newline at end of file

+*.BiocCheck

@@ -1,6 +1,6 @@

 Package: FuseSOM

 Title: A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets

-Version: 0.99.1

+Version: 0.99.2

 Authors@R: 

     person("Elijah", "Willie", , "[email protected]", role = c("aut", "cre"))

 Description: A correlation based multiview self organizing map for the characterization of cell types (`FuseSOM`) 

@@ -36,4 +36,4 @@ VignetteBuilder: knitr

 BugReports: https://github.com/ecool50/FuseSOM/issues

 LinkingTo: Rcpp

 biocViews: 

-    SingleCell, CellBasedAssays, SingleCellExperiment

+    SingleCell, CellBasedAssays

@@ -18,4 +18,4 @@ importFrom(ggplotify,as.ggplot)

 importFrom(pheatmap,pheatmap)

 importFrom(proxy,dist)

 importFrom(psych,cor2dist)

-useDynLib(FuseSOM)

\ No newline at end of file

+useDynLib(FuseSOM)

@@ -92,7 +92,7 @@ normaliseData <- function(data, markers, method='none', cofactor=5){

 #' @examples

 #' data("risom_dat")

 #' risomMarkers <- c('CD45','SMA','CK7','CK5','VIM','CD31','PanKRT','ECAD')

-#' normalizeData(risom_dat[, risomMarkers])

+#' normaliseData(risom_dat[, risomMarkers])

 #' 

 #' @author

 #'   Elijah WIllie <[email protected]>

new file mode 100644

@@ -0,0 +1,15 @@

+#' FuseSOM: FuseSOM provides a pipeline for the clustering of highly

+#' multiplexed in situ imaging cytometry assays. This pipeline uses

+#' the Self Organizing Map architecture coupled with Multiview hierarchical

+#' clustering. We also provide functions for normalisation and estimation

+#' of the number of clusters.

+#'

+#' The FuseSOM package provides three categories of important functions:

+#' foo, bar and baz.

+#'

+#'

+#' @docType package

+#' @name FuseSOM

+#' @useDynLib FuseSOM

+NULL

+#> NULL

\ No newline at end of file

@@ -32,7 +32,6 @@

   # ------ SILHOUETTE

   Sil <- NULL

-  browser()

   if('sil' %in% measures) if(k > 1) Sil <- mean(cluster::silhouette(cl, stats::as.dist(dMat))) else Sil <- 0

   # TODO: Touch base with Elijah to ensure I haven't proken anything 

new file mode 100644

@@ -0,0 +1,14 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/FuseSOM.R

+\docType{package}

+\name{FuseSOM}

+\alias{FuseSOM}

+\title{FuseSOM: FuseSOM provides a pipeline for the clustering of highly

+multiplexed in situ imaging cytometry assays. This pipeline uses

+the Self Organizing Map architecture coupled with Multiview hierarchical

+clustering. We also provide functions for normalisation and estimation

+of the number of clusters.}

+\description{

+The FuseSOM package provides three categories of important functions:

+foo, bar and baz.

+}

@@ -28,7 +28,7 @@ These methods include Percentile, zscore, arsinh and minmax

 \examples{

 data("risom_dat")

 risomMarkers <- c('CD45','SMA','CK7','CK5','VIM','CD31','PanKRT','ECAD')

-normalizeData(risom_dat[, risomMarkers])

+normaliseData(risom_dat[, risomMarkers])

 }

 \author{