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')
