new file mode 100644

@@ -0,0 +1,10 @@

+# Changes in version 0.99.0 (2016-10-23)

+- Submitted to Bioconductor

+

+# Changes in version 1.17.1 (2021-10-14)

+- Changes C backend to C++

+- Adds within -omics subsampling

+- Improves vignette

+- Fixes several bugs

+    - Labels for createVectors() now correct

+    - C (now C++) backend no longer crashes R when things go wrong

\ No newline at end of file

@@ -145,10 +145,10 @@ discordantRun <- function(v1, v2, x, y = NULL, transform = TRUE,

         }

         if (repeats >= floor(iter * .1)) {

-          stop(paste0("\nInsufficient data for subsampling. Increase number of",

+          stop("\nInsufficient data for subsampling. Increase number of",

                "\nfeatures, reduce numberof components used, or increase", 

                "\nsubSize if not at default value. Alternatively, set",

-               "\nsubsampling=FALSE."))

+               "\nsubsampling=FALSE.")

         }

       mu <- total_mu / iter

@@ -165,9 +165,8 @@ discordantRun <- function(v1, v2, x, y = NULL, transform = TRUE,

         pd <- tryCatch({em.normal.partial.concordant(pdata, class, components)},

                        error = function(unused) return(NULL))

         if (is.null(pd)) {

-          stop(

-            paste0("\nInsufficient data for component estimation. Increase",

-                   "\nnumber of features or reduce number of components used."))

+          stop("\nInsufficient data for component estimation. Increase",

+               "\nnumber of features or reduce number of components used.")

         }

         zTable <- pd$z

         classVector <- pd$class

@@ -343,16 +342,16 @@ em.normal.partial.concordant <- function(data, class, components) {

       subSize <- floor(length(rownames(x)) / 2)

     } else if (subSize > floor(length(rownames(x)) / 2)) {

       subSize <- floor(length(rownames(x)) / 2)

-      warning(paste0("subSize argument too large. Using subSize ", subSize,

-                     " See vignette for more information."))

+      warning("subSize argument too large. Using subSize ", subSize,

+              " See vignette for more information.")

     }

   } else {

     if (is.null(subSize)) {

       subSize <- min(nrow(x), nrow(y))

     } else if (subSize > min(nrow(x), nrow(y))) {

       subSize <- min(nrow(x), nrow(y))

-      warning(paste0("subSize argument to large. Using subSize ", subSize,

-                     " See vignette for more information."))

+      warning("subSize argument to large. Using subSize ", subSize,

+              " See vignette for more information.")

     }

   }

   return(subSize)

deleted file mode 100644

@@ -1 +0,0 @@

-October 23, 2016: Package submitted.

@@ -471,22 +471,22 @@ involved in drawing subsamples, and results may differ using different seeds.

 ```{r}

 # Load Data

-data(TCGA_Breast_miRNASeq)

-data(TCGA_Breast_RNASeq)

+data(TCGA_Breast_miRNASeq_voom)

+data(TCGA_Breast_RNASeq_voom)

 # Prepare groups

 groups <- c(rep(1, 15), rep(2, 42))

 # Create correlation vectors

-sub_vectors <- createVectors(x = TCGA_Breast_miRNASeq, 

-                             y = TCGA_Breast_RNASeq,

+sub_vectors <- createVectors(x = TCGA_Breast_miRNASeq_voom, 

+                             y = TCGA_Breast_RNASeq_voom,

                              groups = groups)

 # Run analysis with subsampling

 set.seed(126)

 sub_result <- discordantRun(sub_vectors$v1, sub_vectors$v2,

-                            x = TCGA_Breast_miRNASeq,

-                            y = TCGA_Breast_RNASeq,

+                            x = TCGA_Breast_miRNASeq_voom,

+                            y = TCGA_Breast_RNASeq_voom,

                             components = 3, subsampling = TRUE)

 # Results