setting up git-svn bridge

DESCRIPTION

@@ -1,33 +1,20 @@
 Package: DEGreport
-Version: 0.99.6
+Version: 0.99.7
 Date: 2014-05-2
 Type: Package
 Title: Report of DEG analysis
-Description: Creation of a HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability  for each selected gene.
-biocViews: DifferentialExpression, 
-    Visualization, 
-    RNASeq,
-    ReportWriting
-Suggests:
-    knitr,
-    biomaRt,
-    RUnit,
-    BiocStyle,
-    BiocGenerics
-Depends:
-    R (>= 3.0.0),
-    rjags,
-    quantreg
-Imports:
-    plyr,
-    utils,
-    ggplot2,
-    Nozzle.R1,
-    coda,
-    edgeR
-SystemRequirements:   jags (>= 3.0.0)
+Description: Creation of a HTML report of differential expression
+        analyses of count data. It integrates some of the code
+        mentioned in DESeq2 and edgeR vignettes, and report a ranked
+        list of genes according to the fold changes mean and
+        variability for each selected gene.
+biocViews: DifferentialExpression, Visualization, RNASeq, ReportWriting
+Suggests: knitr, biomaRt, RUnit, BiocStyle, BiocGenerics
+Depends: R (>= 3.0.0), rjags, quantreg
+Imports: plyr, utils, ggplot2, Nozzle.R1, coda, edgeR
+SystemRequirements: jags (>= 3.0.0)
 Author: Lorena Pantano
 Maintainer: Lorena Pantano <[email protected]>
 License: GPL (>=2)
 VignetteBuilder: knitr
-Roxygen: list(wrap = TRUE)
+Roxygen: list(wrap = TRUE)

R/DEGreportSet.R

@@ -1,7 +1,6 @@
 #' @name DEGreportSet
 #' @title list object for DE genes betwen Male and Females
-#' @description list of objects containgin counts matrix,g1,g2 and edgeR glmfit
-#' object
+#' @description list of objects containgin counts matrix,g1,g2 and edgeR glmfit object
 #' @docType data
 #' @usage DEGreportSet
 #' @format matrix,list,list and matrix

R/methods.R

@@ -315,7 +315,7 @@ degBIcmd <-
 #' data(DEGreportSet)
 #' degRank(DEGreportSet$g1,DEGreportSet$g2,
 #'     DEGreportSet$counts[DEGreportSet$detag[1:5],],
-#'     DEGreportSet$deg[DEGreportSet$detag[1:5],1],100,300)
+#'     DEGreportSet$deg[DEGreportSet$detag[1:5],1],400,500)
 degRank <- 
     function(g1,g2,counts,fc,popsize,iter=1000)
 {

R/report.R

@@ -215,13 +215,13 @@ createReport <-
     report  <-  newCustomReport( "DEG Report " );
     report  <-  addTo( 
         report, addTo( newSection( "Quality of DEG", class="results" ),
-                    addTo( newSubSection( "Pvalue vs abundance" ), fg1),
-                    addTo( newSubSection( "Pvalue vs variation" ), fg2),
-                    addTo( newSubSection("Pvalue vs abundance/variation"),fg3),    
-                    addTo( newSubSection( "Abundance distribution" ), fg4),
-                    addTo( newSubSection( "Variation distribution" ), fg5),
-                    addTo( newSubSection("Rank"), tb1),
-                    addTo( newSubSection("FC vs rank"), fg6)
+                       addTo( newSubSection( "Pvalue vs abundance" ), fg1),
+                       addTo( newSubSection( "Pvalue vs variation" ), fg2),
+                       addTo( newSubSection("Pvalue vs abundance/variation"), fg3),    
+                       addTo( newSubSection( "Abundance distribution" ), fg4),
+                       addTo( newSubSection( "Variation distribution" ), fg5),
+                       addTo( newSubSection("Rank"), tb1),
+                       addTo( newSubSection("FC vs rank"), fg6)
         ))
 
     writeReport( report, filename=paste0(path,name))

data/datalist

@@ -0,0 +1,2 @@
+DEGreportSet
+humanSexDEedgeR

man/degRank.Rd

@@ -30,6 +30,6 @@ Get rank data frame with best score on the top
 data(DEGreportSet)
 degRank(DEGreportSet$g1,DEGreportSet$g2,
     DEGreportSet$counts[DEGreportSet$detag[1:5],],
-    DEGreportSet$deg[DEGreportSet$detag[1:5],1],100,300)
+    DEGreportSet$deg[DEGreportSet$detag[1:5],1],400,500)
 }