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

 Package: MineICA

 Type: Package

 Title: Analysis of an ICA decomposition obtained on genomics data

-Version: 1.37.0

+Version: 1.37.1

 Date: 2012-03-16

 Author: Anne Biton

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

@@ -1024,7 +1024,7 @@ plotCorGraph <- function(

     indLowCor <- which(abs(E(ig)$weight)<=0.4)

     E(ig)$weight <- 1/abs(log2(abs(E(ig)$weight)))

     E(ig)$weight[indHighCor] <- E(ig)$weight[indHighCor]+6

-    E(ig)$weight[indLowCor] <- E(ig)$weight[indLowCor]-0.25

+    #E(ig)$weight[indLowCor] <- E(ig)$weight[indLowCor] -0.25

    if (!missing(reciproCol)) {

        if (reciproCol %in% colnames(dataGraph)) {

@@ -267,13 +267,12 @@ hypergeoAn <- function ( icaSet,

 `addGenesToGoReport` <-

 function(hgOver, universe, db = c("GO","KEGG"), onto = c("CC", "MF", "BP"), annotation = NULL, entrez2symbol = NULL) {

-  require(GOstats)

   db <- match.arg(tolower(db), choices = c("go","kegg"))

   onto <- match.arg(toupper(onto), choices = c("CC", "MF", "BP"))

-  a <- geneIdsByCategory(hgOver)

-  b <- geneIdUniverse(hgOver, cond=conditional(hgOver))

+  a <- GOstats::geneIdsByCategory(hgOver)

+  b <- GOstats::geneIdUniverse(hgOver, cond=conditional(hgOver))

   a <- a[sigCategories(hgOver)]

   b <- b[sigCategories(hgOver)]