Merge pull request #24 from BioBam/develop

Develop
BioBam · Dec 27, 2023 · 94a1fdc · 94a1fdc
2 parents bda916e + c42942b
commit 94a1fdc
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Showing 110 changed files with 5,637 additions and 2,797 deletions.
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
diff --git a/.github/workflows/render-rmarkdown.yaml b/.github/workflows/render-rmarkdown.yaml
diff --git a/NAMESPACE b/NAMESPACE
@@ -5,19 +5,20 @@ export("cDense<-")
 export("cSparse<-")
 export("eDense<-")
 export("eSparse<-")
-export(.scmp_show)
-export(as.scmp)
+export(.ScMaSigPro_show)
+export(as_scmp)
 export(bAlloc)
 export(cDense)
 export(cSparse)
-export(create.scmp)
+export(create_scmp)
 export(eDense)
 export(eSparse)
 export(m3_select_path)
 export(plotBinTile)
 export(plotIntersect)
 export(plotTrend)
 export(plotTrendCluster)
+export(sc.cluster.trend)
 export(sc.filter)
 export(sc.get.features)
 export(sc.p.vector)
@@ -32,7 +33,7 @@ export(showPoly)
 export(showSigProf)
 export(showSol)
 export(showTS)
-exportClasses(scmp)
+exportClasses(ScMaSigPro)
 exportMethods("bAlloc<-")
 exportMethods("cDense<-")
 exportMethods("cSparse<-")
@@ -87,6 +88,7 @@ importFrom(maSigPro,make.design.matrix)
 importFrom(maSigPro,position)
 importFrom(maSigPro,reg.coeffs)
 importFrom(magrittr,"%>%")
+importFrom(mclust,Mclust)
 importFrom(methods,as)
 importFrom(methods,is)
 importFrom(methods,new)
@@ -137,7 +139,9 @@ importFrom(shiny,uiOutput)
 importFrom(shiny,verbatimTextOutput)
 importFrom(stats,IQR)
 importFrom(stats,anova)
+importFrom(stats,as.dist)
 importFrom(stats,complete.cases)
+importFrom(stats,cor)
 importFrom(stats,cutree)
 importFrom(stats,dist)
 importFrom(stats,family)
@@ -146,6 +150,7 @@ importFrom(stats,glm)
 importFrom(stats,glm.control)
 importFrom(stats,hclust)
 importFrom(stats,influence.measures)
+importFrom(stats,kmeans)
 importFrom(stats,median)
 importFrom(stats,na.omit)
 importFrom(stats,p.adjust)
@@ -154,6 +159,7 @@ importFrom(stats,sd)
 importFrom(stats,setNames)
 importFrom(stringr,str_remove_all)
 importFrom(stringr,str_split)
+importFrom(stringr,str_split_i)
 importFrom(utils,View)
 importFrom(utils,combn)
 importFrom(utils,data)

diff --git a/R/DESeq2_estimateSizeFactorsForMatrix.R b/R/DESeq2_estimateSizeFactorsForMatrix.R
@@ -1,8 +1,8 @@
 #' @title estimateSizeFactorsForMatrix from DESeq2
 #' @author Simon Anders
 #' Please cite as
-#' Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with
-#' DESeq2 Genome Biology 15(12):550 (2014)
+#' Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and
+#' dispersion for RNA-seq data with DESeq2 Genome Biology 15(12):550 (2014)
 #'
 #' Low-level function to estimate size factors with robust regression.
 #'