diff --git a/DESCRIPTION b/DESCRIPTION index 4d7aa7c..55d7551 100644 --- 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 Depends: R (>= 3.1.0), DESeq2 (>= 1.6.0), edgeR (>= 3.8.0), xtable diff --git a/NEWS b/NEWS index df7e38a..78a601b 100644 --- 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 index f9c05d4..0cbc642 100644 --- 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 index 6f1e177..7462392 100644 --- 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 index e5d85c2..d0a2876 100644 --- 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 index 2ed0f11..b750397 100644 --- 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 index e5d85c2..d0a2876 100644 --- 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 index 2ed0f11..b750397 100644 --- 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 index d8769a5..363edb7 100644 Binary files a/tutorial.pdf and b/tutorial.pdf differ