Merge pull request #4 from PF2-pasteur-fr/development

reportDESeq2
PF2-pasteur-fr · Feb 9, 2015 · 0fe06fa · 0fe06fa
2 parents 921a581 + ad4991a
commit 0fe06fa
Show file tree

Hide file tree

Showing 9 changed files with 15 additions and 9 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: SARTools
 Type: Package
 Title: Statistical Analysis of RNA-Seq Tools
-Version: 1.0.3
-Date: 2015-02-04
+Version: 1.0.4
+Date: 2015-02-09
 Author: Marie-Agnes Dillies and Hugo Varet
 Maintainer: Hugo Varet <[email protected]>
 Depends: R (>= 3.1.0), DESeq2 (>= 1.6.0), edgeR (>= 3.8.0), xtable

diff --git a/NEWS b/NEWS
@@ -1,3 +1,8 @@
+CHANGES IN VERSION 1.0.4
+------------------------
+	o Order counts according to features names in loadCountData()
+	o Small modifications in the DESeq2 report due to the changes in version 1.0.3
+
 CHANGES IN VERSION 1.0.3
 ------------------------
 	o If use of DESeq2, the cooksCutoff parameter is now TRUE or FALSE (instead of NULL, Inf or a numeric)

diff --git a/R/loadCountData.R b/R/loadCountData.R
@@ -34,6 +34,7 @@ loadCountData <- function(target, rawDir="raw", header=FALSE, skip=0,
   rawCounts[is.na(rawCounts)] <- 0
   counts <- as.matrix(rawCounts[,-1])
   rownames(counts) <- rawCounts[,1]
+  counts <- counts[order(rownames(counts)),]
 
   cat("\nFeatures removed:\n")
   for (f in featuresToRemove){

diff --git a/inst/report_DESeq2.rmd b/inst/report_DESeq2.rmd
@@ -194,7 +194,7 @@ DESeq2 aims at fitting one linear model per feature. For this project, the desig
 
 ### 5.2 Outlier detection
 
-Model outliers are features for which at least one sample seems unrelated to the experimental or study design. For every feature and for every sample, the Cook's distance [Cook, 1977] reflects how the sample matches the model. A large value of the Cook's distance indicates an outlier count and p-values are not computed for the corresponding feature. `r ifelse(!is.null(cooksCutoff) && is.infinite(cooksCutoff),"For this project, the detection of model outliers have been turned off by setting the cut-off to the infinite.","")`
+Model outliers are features for which at least one sample seems unrelated to the experimental or study design. For every feature and for every sample, the Cook's distance [Cook, 1977] reflects how the sample matches the model. A large value of the Cook's distance indicates an outlier count and p-values are not computed for the corresponding feature. `r ifelse(!cooksCutoff,"For this project, the detection of model outliers have been turned off by setting the cut-off to the infinite.","")`
 
 ### 5.3 Dispersions estimation
 
@@ -229,7 +229,7 @@ if (independentFiltering){
   cat("Table 6 reports the thresholds used for each comparison and the number of features discarded by the independent filtering. Adjusted p-values of discarded features are then set to NA.\n")
   print(xtable(summaryResults$tabIndepFiltering,caption="Table 6: Number of features discarded by the independent filtering for each comparison."),type="html",include.rownames=FALSE, html.table.attributes = "align='center'")
 } else{
-  cat("For this project, no independent filtering has been performed.\\\\")
+  cat("For this project, no independent filtering has been performed.")
 }
 ```
 
@@ -307,7 +307,7 @@ Parameter values used for this analysis are:
 - condRef: `r condRef`
 - batch: `r ifelse(is.null(batch),"NULL",batch)`
 - fitType: `r fitType`
-- cooksCutoff: `r ifelse(is.null(cooksCutoff),"NULL",cooksCutoff)`
+- cooksCutoff: `r cooksCutoff`
 - independentFiltering: `r independentFiltering`
 - alpha: `r alpha`
 - pAdjustMethod: `r pAdjustMethod`

diff --git a/inst/template_script_DESeq2.r b/inst/template_script_DESeq2.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and DESeq2 packages
 ### Hugo Varet
 ### February 04th, 2015
-### designed to be executed with SARTools 1.0.3
+### designed to be executed with SARTools 1.0.4
 ################################################################################
 
 ################################################################################

diff --git a/inst/template_script_edgeR.r b/inst/template_script_edgeR.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and edgeR packages
 ### Hugo Varet
 ### February 04th, 2015
-### designed to be executed with SARTools 1.0.3
+### designed to be executed with SARTools 1.0.4
 ################################################################################
 
 ################################################################################

diff --git a/template_script_DESeq2.r b/template_script_DESeq2.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and DESeq2 packages
 ### Hugo Varet
 ### February 04th, 2015
-### designed to be executed with SARTools 1.0.3
+### designed to be executed with SARTools 1.0.4
 ################################################################################
 
 ################################################################################

diff --git a/template_script_edgeR.r b/template_script_edgeR.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and edgeR packages
 ### Hugo Varet
 ### February 04th, 2015
-### designed to be executed with SARTools 1.0.3
+### designed to be executed with SARTools 1.0.4
 ################################################################################
 
 ################################################################################

diff --git a/tutorial.pdf b/tutorial.pdf