@@ -1,8 +1,8 @@

 Package: MineICA

 Type: Package

 Title: Analysis of an ICA decomposition obtained on genomics data

-Version: 0.1.0

-Date: 2012-01-21

+Version: 0.99.1

+Date: 2012-03-16

 Author: Anne Biton

 Maintainer: <anne.biton@gmail.com>

 Description: The goal of MineICA is to make easier the interpretation of the

@@ -14,17 +14,58 @@ Description: The goal of MineICA is to make easier the interpretation of the

 License: GPL-2

 LazyLoad: yes

 BiocViews: Bioinformatics, Visualizations, MultipleComparisons

-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

+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

 Enhances: doMC

-Collate: 'AllClasses.R' 'AllGeneric.R' 'methods-IcaSet.R'

-        'methods-MineICAParams.R' 'compareAnalysis.R'

-        'functions_comp2annot.R' 'functions_comp2annottests.R'

-        'functions_enrich.R' 'functions.R' 'heatmap.plus.R'

-        'heatmapsOnSel.R' 'runAn.R' 'compareGenes.R'

+Collate:

+    'AllClasses.R'

+    'AllGeneric.R'

+    'methods-IcaSet.R'

+    'methods-MineICAParams.R'

+    'compareAnalysis.R'

+    'functions_comp2annot.R'

+    'functions_comp2annottests.R'

+    'functions_enrich.R'

+    'functions.R'

+    'heatmap.plus.R'

+    'heatmapsOnSel.R'

+    'runAn.R'

+    'compareGenes.R'

@@ -399,7 +399,7 @@ plotAllMix <- function (mc, A, nbMix = NULL, pdf,  nbBreaks = 20, xlim=NULL) {

         if (!missing(pdf))

-            pdf(file, width = 9, height = 9, title=file)

+            pdf(pdf, width = 9, height = 9, title=file)

 	par(mfrow = c(3,3))