diff --git a/DEGQA.Rproj b/DEGQA.Rproj deleted file mode 100644 index b37945b..0000000 --- a/DEGQA.Rproj +++ /dev/null @@ -1,19 +0,0 @@ -Version: 1.0 - -RestoreWorkspace: No -SaveWorkspace: No -AlwaysSaveHistory: No - -EnableCodeIndexing: Yes -UseSpacesForTab: Yes -NumSpacesForTab: 4 -Encoding: UTF-8 - -RnwWeave: Sweave -LaTeX: pdfLaTeX - -BuildType: Package -PackageInstallArgs: --no-multiarch --with-keep.source -PackageBuildArgs: --resave-data -PackageCheckArgs: --timings --no-build-vignettes -PackageRoxygenize: rd diff --git a/DESCRIPTION b/DESCRIPTION index 3fdb33c..e8a58d1 100644 --- a/DESCRIPTION +++ b/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 License: GPL (>=2) VignetteBuilder: knitr -Roxygen: list(wrap = TRUE) \ No newline at end of file +Roxygen: list(wrap = TRUE) diff --git a/R/DEGreportSet.R b/R/DEGreportSet.R index a3654cc..b41a7d0 100644 --- a/R/DEGreportSet.R +++ b/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 diff --git a/R/methods.R b/R/methods.R index 29abbd5..c1281d2 100644 --- a/R/methods.R +++ b/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) { diff --git a/R/report.R b/R/report.R index cf70e9b..668ae62 100644 --- a/R/report.R +++ b/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)) diff --git a/data/datalist b/data/datalist new file mode 100644 index 0000000..a250d73 --- /dev/null +++ b/data/datalist @@ -0,0 +1,2 @@ +DEGreportSet +humanSexDEedgeR diff --git a/data/humanSexDEedgeR.rda b/data/humanSexDEedgeR.rda index b4bd24f..97d88e4 100644 Binary files a/data/humanSexDEedgeR.rda and b/data/humanSexDEedgeR.rda differ diff --git a/man/degRank.Rd b/man/degRank.Rd index 4448827..2e98aef 100644 --- a/man/degRank.Rd +++ b/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) } diff --git a/vignettes/DEGreportHTML.rmd b/vignettes/DEGreportHTML.Rmd similarity index 100% rename from vignettes/DEGreportHTML.rmd rename to vignettes/DEGreportHTML.Rmd