CHANGES IN VERSION 1.29.2 ------------------------------ MINOR MODIFICATION o minor update of the 'show' method CHANGES IN VERSION 1.25.6 ------------------------------ MINOR MODIFICATION o minor modification update CHANGES IN VERSION 1.25.4 ------------------------------ MINOR MODIFICATION o biosigner.Rmd vignette: update CHANGES IN VERSION 1.25.2 ------------------------------ NEW FEATURE o biosign: now handles SummarizedExperiment and MultiAssayExperiment instances CHANGES IN VERSION 1.19.2 ------------------------------ MINOR MODIFICATION o getMset: minor correction in documentation CHANGES IN VERSION 1.17.2 ------------------------------ MINOR MODIFICATION o getMset: minor correction in documentation CHANGES IN VERSION 1.15.4 ------------------------------ MINOR MODIFICATION o biosigner.Rmd vignette: minor update CHANGES IN VERSION 1.15.2 ------------------------------ NEW FEATURE o biosigner.Rmd vignette: ropls::view method replaces ropls::strF (deprecated) CHANGES IN VERSION 1.13.20 ------------------------------ BUG FIXED o plot.biosignMultiDataSet correction to include all plots in the .pdf file CHANGES IN VERSION 1.13.18 ------------------------------ MINOR MODIFICATION o Minor correction in the plot.biosignMultiDataSet documentation CHANGES IN VERSION 1.13.16 ------------------------------ MINOR MODIFICATION o Minor correction in the biosignMultiDataSet class documentation CHANGES IN VERSION 1.13.14 ------------------------------ MINOR MODIFICATION o Minor correction in the biosignMultiDataSet class documentation CHANGES IN VERSION 1.13.12 ------------------------------ INTERNAL MODIFICATION o Minor internal modification CHANGES IN VERSION 1.13.10 ------------------------------ INTERNAL MODIFICATION o Minor internal modification CHANGES IN VERSION 1.13.8 ------------------------------ NEW FEATURE o final call to warnings() omitted CHANGES IN VERSION 1.13.6 ------------------------------ NEW FEATURES o seedI argument now available (set to 123 by default) o biosign can now be applied to MultiDataSet objects (getMset method to get the updated MultiDataSet back) CHANGES IN VERSION 1.13.4 ------------------------------ MINOR MODIFICATION o minor internal modification CHANGES IN VERSION 1.13.2 ------------------------------ NEW FEATURE o info.txtC and fig.pdfC argument values NULL and NA replaced by 'none' and 'interactive', respectively CHANGES IN VERSION 1.11.26 ------------------------------ NEW FEATURE o biosign and plot methods: 'fig.pdfC' and 'info.txtC' arguments have been added for compatibility reasons with other packages; they have the same role as 'file.pdfC' and '.sinkC' which now generate a deprecated warning. CHANGES IN VERSION 1.11.24 ------------------------------ MINOR MODIFICATION o minor internal modification CHANGES IN VERSION 1.11.22 ------------------------------ MINOR MODIFICATION o minor internal modification CHANGES IN VERSION 1.11.20 ------------------------------ MINOR MODIFICATION o minor internal modification CHANGES IN VERSION 1.11.18 ------------------------------ MINOR MODIFICATION o minor internal modification CHANGES IN VERSION 1.11.16 ------------------------------ MINOR MODIFICATION o minor internal modification for the handling of ExpressionSet instances CHANGES IN VERSION 1.11.14 ------------------------------ MINOR MODIFICATION o minor internal modification CHANGES IN VERSION 1.11.12 ------------------------------ MINOR MODIFICATION o minor modification in the example of application to ExpressionSet instances CHANGES IN VERSION 1.11.10 ------------------------------ MINOR MODIFICATION o minor update of example CHANGES IN VERSION 1.11.8 ------------------------------ MINOR MODIFICATION o vignette minor modification CHANGES IN VERSION 1.11.6 ------------------------------ MINOR MODIFICATION o dev.new() is no more called by the plot method CHANGES IN VERSION 1.11.4 ------------------------------ BUG FIXED o error message when y is a character but not a factor is now fixed CHANGES IN VERSION 1.11.2 ------------------------------ NEW FEATURES o Application to ExpressionSet: tiers now returned in the fData CHANGES IN VERSION 1.7.4 ------------------------------ INTERNAL MODIFICATIONS o unit testing on Windows 32 bits disabled CHANGES IN VERSION 1.7.2 ------------------------------ INTERNAL MODIFICATIONS o modification in unit testing CHANGES IN VERSION 1.3.6 ------------------------------ INTERNAL MODIFICATIONS o minor internal modification for compatibility with the Galaxy module CHANGES IN VERSION 1.3.4 ------------------------------ MINOR MODIFICATIONS o minor modification in vignette CHANGES IN VERSION 1.3.2 ------------------------------ MINOR MODIFICATIONS o vignette now in pdf format CHANGES IN VERSION 1.1.14 ------------------------------ INTERNAL MODIFICATIONS o Biobase import restricted to ExpressionSet, exprs, and pData function/methods to avoid warning (conflict on 'combine' with randomForest) CHANGES IN VERSION 1.1.12 ------------------------------ INTERNAL MODIFICATIONS o minor modification in unit tests CHANGES IN VERSION 1.1.10 ------------------------------ NEW FEATURE o biosign can now be applied to an ExpressionSet object o vignette in html format INTERNAL MODIFICATIONS o documentation generated with roxygen2 and vignette with rmarkdown CHANGES IN VERSION 1.1.8 ------------------------------ INTERNAL MODIFICATIONS o error message fixed when missing values in the accuracy vector obtained by the bootstrap step CHANGES IN VERSION 1.1.6 ------------------------------ INTERNAL MODIFICATIONS o versioning update o unit tests silenced on windows platforms because of errors on the moscato2 bioc platform running on windows 8 CHANGES IN VERSION 1.1.4 ------------------------------ INTERNAL MODIFICATIONS o bug fixed (when tierMN contains 0 only) o 'show' method: better handling of messages when no signature is found CHANGES IN VERSION 1.1.2 ------------------------------ INTERNAL MODIFICATIONS o unit tests: test_biosign_diaplasma and test_biosign_sacurine added o internal renaming of variables (to indicate their type) and functions (to facilitate their understanding) o PLS-DA: to avoid errors during generation of models, the number of predictive components is at least 1 CHANGES IN VERSION 1.1.0 ------------------------------ PACKAGE MODIFICATION o Wellcome to the biosigner package for feature selection from omics datasets o The package implements a new wrapper method detecting the features which are important for PLS-DA, Random Forest, or SVM binary classification o The package contains the 'diaplasma' LC-MS metabolomics real dataset (plasma samples from diabetic type 1 and 2 patients) o Please see the vignette for details about the approach and package use o The corresponding publication is currently under review. CHANGES IN VERSION 0.99.11 ------------------------------ BUG FIXED o in vignette (due to switch in S4 methods for ropls) CHANGES IN VERSION 0.99.10 ------------------------------ PACKAGE MODIFICATION o grDevices, graphics, stats, utils imported in DESCRIPTION CHANGES IN VERSION 0.99.9 ------------------------------ PACKAGE MODIFICATION o vignette update CHANGES IN VERSION 0.99.8 ------------------------------ PACKAGE MODIFICATION o adding the import of the following function in NAMESPACE: abline arrows axis box boxplot dev.new dev.off head image layout median mtext par pdf rect tail title var o defining the getAccuracyMN and getSignatureLs accessors CHANGES IN VERSION 0.99.7 ------------------------------ PACKAGE MODIFICATION o additional unit test silenced in test_biosign_randomforest (because of errors on the moscato2 Windows 2008 platform) CHANGES IN VERSION 0.99.6 ------------------------------ PACKAGE MODIFICATION o unit tests silenced in test_biosign_randomforest and test_biosign_predict (because of errors on the moscato2 Windows 2008 platform) CHANGES IN VERSION 0.99.5 ------------------------------ PACKAGE MODIFICATION o importing of packages in NAMESPACE fixed o use of S4 methods (instead of S3) CHANGES IN VERSION 0.99.4 ------------------------------ PACKAGE MODIFICATION o correction of a bug in the test_biosign_plsdaF test function CHANGES IN VERSION 0.99.0 ------------------------------ PACKAGE MODIFICATION o set version number to 0.99.0 for Bioconductor CHANGES IN VERSION 0.5.13 ------------------------------ NEW FEATURES o biosign: printing messages (for development purpose) removed CHANGES IN VERSION 0.5.12 ------------------------------ NEW FEATURES o biosign: new ordering of tierMC (previsously by decreasing row sums): now rows containing maximum tier are first grouped, before being ordered by decreasing row sums within each group o biosign: remove deprecated CV functions and their calls; remove deprecated arguments CHANGES IN VERSION 0.5.11 ------------------------------ NEW FEATURES o diaplasma dataset: minor changes in variable names (column names of dataMatrix and row names of variableMetadata) CHANGES IN VERSION 0.5.10 ------------------------------ NEW FEATURES o unit tests: now run on 'diaplasma' dataset (instead of 'sacurine' from the 'ropls' package) CHANGES IN VERSION 0.5.9 ------------------------------ NEW FEATURES o predict.biosign: predictions on 'S+A' signatures now possible BUG FIXES o diaplasma dataset: formatting of dataMatrix column names (and variableMetadata row names) CHANGES IN VERSION 0.5.8 ------------------------------ NEW FEATURES o diaplasma dataset: annotations (when available) annotated to column names of dataMatrix (and row names of variableMetadata) CHANGES IN VERSION 0.5.7 ------------------------------ BUG FIXES o biosign: now correctly attribute grade from score when one or more methods has no S variables o plot.biosign: management of errors when signatures are empty CHANGES IN VERSION 0.5.6 ------------------------------ NEW FEATURES o biosign: now call itself on the best half variables when no significant variables are found o biosign: now produce grade A and less when no S are produced BUG FIXES o biosign: remove an unnecessary test in the 'translate' code CHANGES IN VERSION 0.5.5 ------------------------------ NEW FEATURES o biosign: now correctly handle non significant rank/results for one or two methods when at least one other is significant BUG FIXES o now ensure 20% of out of the bag samples in the bootstrap extraction o predict: handling void signatures in predictions CHANGES IN VERSION 0.5.4 ------------------------------ NEW FEATURES o minor modifications CHANGES IN VERSION 0.5.3 ------------------------------ NEW FEATURES o minor modifications CHANGES IN VERSION 0.5.2 ------------------------------ NEW FEATURES o first complete version of the package (including the vignette) CHANGES IN VERSION 0.5.1 ------------------------------ NEW FEATURES o diaplasma dataset added CHANGES IN VERSION 0.4.13 ------------------------------ NEW FEATURES o plot: new typeC = "boxplot" argument for plotting the individual features from the signature o first draft of vignette CHANGES IN VERSION 0.4.12 ------------------------------ NEW FEATURES o 'predict' method now available CHANGES IN VERSION 0.4.11 ------------------------------ NEW FEATURES o 'AS' model and signature returned as outputs from 'biosign' o variables with NA are removed from the 'x' matrix prior to Random Forest and SVM modeling o if missing, 'x' column names are set to 'V1', ..., 'Vp' (where p is the number of variables) o 'x' data frame converted to a matrix (generates a warning) o 'y' character vector converted to a factor (generates a warning) CHANGES IN VERSION 0.4.10 ------------------------------ NEW FEATURES o new argument checks added CHANGES IN VERSION 0.4.9 ------------------------------ NEW FEATURES o signatures from S and AS models returned by biosign CHANGES IN VERSION 0.4.8 ------------------------------ BUG FIXES o in case of no significant variable found, a message is returned (instead of an error) CHANGES IN VERSION 0.4.7 ------------------------------ NEW FEATURES o unit tests updated CHANGES IN VERSION 0.4.6 ------------------------------ BUG FIXES o minor bug corrections in biosign (accuracy output) and plot.biosign (tiers colors) CHANGES IN VERSION 0.4.5 ------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o biosign: accuracy of the 'S+A' model is now computed (in addition to the full and 'S' models) o plot.biosign: 'S' tiers displayed by default (in addition to 'A' when at least one of the restricted models has an accuracy < 80% CHANGES IN VERSION 0.4.4 ------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o plot.biosign: redesigned to display the tiers ('S' and 'A' by default) CHANGES IN VERSION 0.4.3 ------------------------------ NEW FEATURES o biosign: binary search implemented to speed up the search for the number of features CHANGES IN VERSION 0.4.2 ------------------------------ NEW FEATURES o signatures of only one feature are now possible CHANGES IN VERSION 0.4.1 ------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o new names: package: 'biosigner' (instead of 'rdiagnosign') main method and class: 'biosign' (instead of 'diagnosign') o biosign: new 'recursiveL' argument to obtain shorter and more stable signatures CHANGES IN VERSION 0.3.8 ------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o diasgnosign: Full and restricted models now available in the outputs CHANGES IN VERSION 0.3.7 ------------------------------ NEW FEATURES o Change the evaluation method: now compute the balanced classification rate. CHANGES IN VERSION 0.3.6 ------------------------------ NEW FEATURES o unit tests added CHANGES IN VERSION 0.3.5 ------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o 'diagnosign' 'randomforest' method now available CHANGES IN VERSION 0.3.4 ------------------------------ NEW FEATURES o Galaxy module for rdiagnosign has been developed o ggplot2 removed from dependencies (since it is not used currently) CHANGES IN VERSION 0.3.3 ------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o renaming some of the 'dignosign' arguments for simplicity crossValI -> crossvalI nbootI -> bootI permutationI -> permI pvalThreshN -> pvalN CHANGES IN VERSION 0.3.2 ------------------------------ NEW FEATURES o bootstraping included into 'diagnosign' (instead of cross-validation) CHANGES IN VERSION 0.3.1 ------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o package renamed: 'rdiagnosign' (instead of 'multimark') class 'diagnosign' methods 'diagnosign', 'print.diagnosign', 'plot.diagnosign' CHANGES IN VERSION 0.2.3 ------------------------------ NEW FEATURES o internal parameter 'alpha' set to 0.05 instead of 0 CHANGES IN VERSION 0.2.2 ------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o 'signastic' function (replaces 'fsi'): to compute significant features and corresponding models CHANGES IN VERSION 0.2.1 ------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o rename data set tables proMN -> dataMatrix obsDF -> sampleMetadata feaDF -> variableMetadata CHANGES IN VERSION 0.2.0 ------------------------------ NEW FEATURES o 'pls' method available (in addition to 'svm')