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

 Package: MineICA

 Type: Package

 Title: Analysis of an ICA decomposition obtained on genomics data

-Version: 1.7.0

+Version: 1.7.1

 Date: 2012-03-16

 Author: Anne Biton

 Maintainer: Anne Biton <anne.biton@gmail.com>

@@ -15,11 +15,11 @@ Description: The goal of MineICA is to perform Independent Component

         graph.

 License: GPL-2

 LazyLoad: yes

+Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr,

+        ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster,

+        marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph,

+        annotate, Hmisc, fastICA, JADE

 Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db

-Depends: R (>= 2.10), Biobase, plyr, ggplot2, scales, foreach, xtable,

-        biomaRt, gtools, GOstats, cluster, marray, mclust,

-        RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate,

-        Hmisc, fastICA, JADE, methods

 Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph,

         breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP,

         breastCancerVDX

@@ -45,9 +45,6 @@ setGeneric ( "chipManu<-" , function ( object, value ){ standardGeneric ( "chipM

 setGeneric ( "getTypeID" , function ( object ){ standardGeneric ( "getTypeID" )})

 setGeneric ( "typeID<-" , function ( object, value){ standardGeneric ( "typeID<-" )})

 setGeneric ( "typeID" , function ( object ){ standardGeneric ( "typeID" )})

-setGeneric ( "getOrganism" , function ( object ){ standardGeneric ( "getOrganism" )})

-setGeneric ( "organism<-" , function ( object, value){ standardGeneric ( "organism<-" )})

-setGeneric ( "organism" , function ( object ){ standardGeneric ( "organism" )})

 setGeneric ( "getMart" , function ( object ){ standardGeneric ( "getMart" )})

 setGeneric ( "mart<-" , function ( object, value){ standardGeneric ( "mart<-" )})

 setGeneric ( "mart" , function ( object ){ standardGeneric ( "mart" )})

@@ -72,8 +69,6 @@ setGeneric ( "setPackage<-" , function ( object, value ){ standardGeneric ( "set

 setGeneric ( "package<-" , function ( object, value ){ standardGeneric ( "package<-" )})

 setGeneric ( "setTypeID<-" , function ( object, value ){ standardGeneric ( "setTypeID<-" )})

 setGeneric ( "typeID<-" , function ( object, value ){ standardGeneric ( "typeID<-" )})

-setGeneric ( "setOrganism<-" , function ( object, value ){ standardGeneric ( "setOrganism<-" )})

-setGeneric ( "organism<-" , function ( object, value ){ standardGeneric ( "organism<-" )})

 setGeneric ( "setMart<-" , function ( object, value ){ standardGeneric ( "setMart<-" )})

 setGeneric ( "mart<-" , function ( object, value ){ standardGeneric ( "mart<-" )})

@@ -553,12 +553,6 @@ setMethod( "organism" ,"IcaSet" ,

       }

 )

-setMethod( "getOrganism" ,"IcaSet" ,

-       function (object){

-           return (object@organism)

-      }

-)

-

 setMethod( "mart" ,"IcaSet" ,

        function (object){

            return (object@mart)

@@ -873,17 +867,6 @@ setReplaceMethod( f="mart",

       }

 )

-setReplaceMethod( f="setOrganism",

-      signature = "IcaSet" ,

-       definition = function (object, value){

-           object@organism <- value

-           validObject (object)

-           return (object)

-      }

-)

-

-

-

 setReplaceMethod(

       f = "package" ,

       signature = "IcaSet" ,

@@ -23,10 +23,6 @@

 \alias{organism<-}

 \alias{organism,IcaSet-method}

 \alias{organism<-,IcaSet-method}

-\alias{organism<-,IcaSet,character-method}

-\alias{setOrganism,IcaSet-method}

-\alias{getOrganism,IcaSet-method}

-

 \alias{mart}

 \alias{mart<-}