NEWS

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biosigner 1.29.2

MINOR MODIFICATION

• minor update of the 'show' method

biosigner 1.25.6

MINOR MODIFICATION

• minor modification update

biosigner 1.25.4

MINOR MODIFICATION

• biosigner.Rmd vignette: update

biosigner 1.25.2

NEW FEATURE

• biosign: now handles SummarizedExperiment and MultiAssayExperiment instances

biosigner 1.19.2

MINOR MODIFICATION

• getMset: minor correction in documentation

biosigner 1.17.2

MINOR MODIFICATION

• getMset: minor correction in documentation

biosigner 1.15.4

MINOR MODIFICATION

• biosigner.Rmd vignette: minor update

biosigner 1.15.2

NEW FEATURE

• biosigner.Rmd vignette: ropls::view method replaces ropls::strF (deprecated)

biosigner 1.13.20

BUG FIXED

• plot.biosignMultiDataSet correction to include all plots in the .pdf file

biosigner 1.13.18

MINOR MODIFICATION

• Minor correction in the plot.biosignMultiDataSet documentation

biosigner 1.13.16

MINOR MODIFICATION

• Minor correction in the biosignMultiDataSet class documentation

biosigner 1.13.14

MINOR MODIFICATION

• Minor correction in the biosignMultiDataSet class documentation

biosigner 1.13.12

INTERNAL MODIFICATION

• Minor internal modification

biosigner 1.13.10

INTERNAL MODIFICATION

• Minor internal modification

biosigner 1.13.8

NEW FEATURE

• final call to warnings() omitted

biosigner 1.13.6

NEW FEATURES

• seedI argument now available (set to 123 by default)
• biosign can now be applied to MultiDataSet objects (getMset method to get the updated MultiDataSet back)

biosigner 1.13.4

MINOR MODIFICATION

• minor internal modification

biosigner 1.13.2

NEW FEATURE

• info.txtC and fig.pdfC argument values NULL and NA replaced by 'none' and 'interactive', respectively

biosigner 1.11.26

NEW FEATURE

• 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.

biosigner 1.11.24

MINOR MODIFICATION

• minor internal modification

biosigner 1.11.22

MINOR MODIFICATION

• minor internal modification

biosigner 1.11.20

MINOR MODIFICATION

• minor internal modification

biosigner 1.11.18

MINOR MODIFICATION

• minor internal modification

biosigner 1.11.16

MINOR MODIFICATION

• minor internal modification for the handling of ExpressionSet instances

biosigner 1.11.14

MINOR MODIFICATION

• minor internal modification

biosigner 1.11.12

MINOR MODIFICATION

• minor modification in the example of application to ExpressionSet instances

biosigner 1.11.10

MINOR MODIFICATION

• minor update of example

biosigner 1.11.8

MINOR MODIFICATION

• vignette minor modification

biosigner 1.11.6

MINOR MODIFICATION

• dev.new() is no more called by the plot method

biosigner 1.11.4

BUG FIXED

• error message when y is a character but not a factor is now fixed

biosigner 1.11.2

NEW FEATURES

• Application to ExpressionSet: tiers now returned in the fData

biosigner 1.7.4

INTERNAL MODIFICATIONS

• unit testing on Windows 32 bits disabled

biosigner 1.7.2

INTERNAL MODIFICATIONS

• modification in unit testing

biosigner 1.3.6

INTERNAL MODIFICATIONS

• minor internal modification for compatibility with the Galaxy module

biosigner 1.3.4

MINOR MODIFICATIONS

• minor modification in vignette

biosigner 1.3.2

MINOR MODIFICATIONS

• vignette now in pdf format

biosigner 1.1.14

INTERNAL MODIFICATIONS

• Biobase import restricted to ExpressionSet, exprs, and pData function/methods to avoid warning (conflict on 'combine' with randomForest)

biosigner 1.1.12

INTERNAL MODIFICATIONS

• minor modification in unit tests

biosigner 1.1.10

NEW FEATURE

• biosign can now be applied to an ExpressionSet object
• vignette in html format

INTERNAL MODIFICATIONS

• documentation generated with roxygen2 and vignette with rmarkdown

biosigner 1.1.8

INTERNAL MODIFICATIONS

• error message fixed when missing values in the accuracy vector obtained by the bootstrap step

biosigner 1.1.6

INTERNAL MODIFICATIONS

• versioning update
• unit tests silenced on windows platforms because of errors on the moscato2 bioc platform running on windows 8

biosigner 1.1.4

INTERNAL MODIFICATIONS

• bug fixed (when tierMN contains 0 only)
• 'show' method: better handling of messages when no signature is found

biosigner 1.1.2

INTERNAL MODIFICATIONS

• unit tests: test_biosign_diaplasma and test_biosign_sacurine added
• internal renaming of variables (to indicate their type) and functions (to facilitate their understanding)
• PLS-DA: to avoid errors during generation of models, the number of predictive components is at least 1

biosigner 1.1.0

PACKAGE MODIFICATION

• Wellcome to the biosigner package for feature selection from omics datasets
• The package implements a new wrapper method detecting the features which are important for PLS-DA, Random Forest, or SVM binary classification
• The package contains the 'diaplasma' LC-MS metabolomics real dataset (plasma samples from diabetic type 1 and 2 patients)
• Please see the vignette for details about the approach and package use
• The corresponding publication is currently under review.

biosigner 0.99.11

BUG FIXED

• in vignette (due to switch in S4 methods for ropls)

biosigner 0.99.10

PACKAGE MODIFICATION

• grDevices, graphics, stats, utils imported in DESCRIPTION

biosigner 0.99.9

PACKAGE MODIFICATION

• vignette update

biosigner 0.99.8

PACKAGE MODIFICATION

• 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
• defining the getAccuracyMN and getSignatureLs accessors

biosigner 0.99.7

PACKAGE MODIFICATION

• additional unit test silenced in test_biosign_randomforest (because of errors on the moscato2 Windows 2008 platform)

biosigner 0.99.6

PACKAGE MODIFICATION

• unit tests silenced in test_biosign_randomforest and test_biosign_predict (because of errors on the moscato2 Windows 2008 platform)

biosigner 0.99.5

PACKAGE MODIFICATION

• importing of packages in NAMESPACE fixed
• use of S4 methods (instead of S3)

biosigner 0.99.4

PACKAGE MODIFICATION

• correction of a bug in the test_biosign_plsdaF test function

biosigner 0.99.0

PACKAGE MODIFICATION

• set version number to 0.99.0 for Bioconductor

biosigner 0.5.13

NEW FEATURES

• biosign: printing messages (for development purpose) removed

biosigner 0.5.12

NEW FEATURES

• 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
• biosign: remove deprecated CV functions and their calls; remove deprecated arguments

biosigner 0.5.11

NEW FEATURES

• diaplasma dataset: minor changes in variable names (column names of dataMatrix and row names of variableMetadata)

biosigner 0.5.10

NEW FEATURES

• unit tests: now run on 'diaplasma' dataset (instead of 'sacurine' from the 'ropls' package)

biosigner 0.5.9

NEW FEATURES

• predict.biosign: predictions on 'S+A' signatures now possible

BUG FIXES

• diaplasma dataset: formatting of dataMatrix column names (and variableMetadata row names)

biosigner 0.5.8

NEW FEATURES

• diaplasma dataset: annotations (when available) annotated to column names of dataMatrix (and row names of variableMetadata)

biosigner 0.5.7

BUG FIXES

• biosign: now correctly attribute grade from score when one or more methods has no S variables
• plot.biosign: management of errors when signatures are empty

biosigner 0.5.6

NEW FEATURES

• biosign: now call itself on the best half variables when no significant variables are found
• biosign: now produce grade A and less when no S are produced

BUG FIXES

• biosign: remove an unnecessary test in the 'translate' code

biosigner 0.5.5

NEW FEATURES

• biosign: now correctly handle non significant rank/results for one or two methods when at least one other is significant

BUG FIXES

• now ensure 20% of out of the bag samples in the bootstrap extraction
• predict: handling void signatures in predictions

biosigner 0.5.4

NEW FEATURES

• minor modifications

biosigner 0.5.3

NEW FEATURES

• minor modifications

biosigner 0.5.2

NEW FEATURES

• first complete version of the package (including the vignette)

biosigner 0.5.1

NEW FEATURES

• diaplasma dataset added

biosigner 0.4.13

NEW FEATURES

• plot: new typeC = "boxplot" argument for plotting the individual features from the signature
• first draft of vignette

biosigner 0.4.12

NEW FEATURES

• 'predict' method now available

biosigner 0.4.11

NEW FEATURES

• 'AS' model and signature returned as outputs from 'biosign'
• variables with NA are removed from the 'x' matrix prior to Random Forest and SVM modeling
• if missing, 'x' column names are set to 'V1', ..., 'Vp' (where p is the number of variables)
• 'x' data frame converted to a matrix (generates a warning)
• 'y' character vector converted to a factor (generates a warning)

biosigner 0.4.10

NEW FEATURES

• new argument checks added

biosigner 0.4.9

NEW FEATURES

• signatures from S and AS models returned by biosign

biosigner 0.4.8

BUG FIXES

• in case of no significant variable found, a message is returned (instead of an error)

biosigner 0.4.7

NEW FEATURES

• unit tests updated

biosigner 0.4.6

BUG FIXES

• minor bug corrections in biosign (accuracy output) and plot.biosign (tiers colors)

biosigner 0.4.5

SIGNIFICANT USER-VISIBLE CHANGES

• biosign: accuracy of the 'S+A' model is now computed (in addition to the full and 'S' models)
• plot.biosign: 'S' tiers displayed by default (in addition to 'A' when at least one of the restricted models has an accuracy < 80%

biosigner 0.4.4

SIGNIFICANT USER-VISIBLE CHANGES

• plot.biosign: redesigned to display the tiers ('S' and 'A' by default)

biosigner 0.4.3

NEW FEATURES

• biosign: binary search implemented to speed up the search for the number of features

biosigner 0.4.2

NEW FEATURES

• signatures of only one feature are now possible

biosigner 0.4.1

SIGNIFICANT USER-VISIBLE CHANGES

• new names: package: 'biosigner' (instead of 'rdiagnosign') main method and class: 'biosign' (instead of 'diagnosign')
• biosign: new 'recursiveL' argument to obtain shorter and more stable signatures

biosigner 0.3.8

SIGNIFICANT USER-VISIBLE CHANGES

• diasgnosign: Full and restricted models now available in the outputs

biosigner 0.3.7

NEW FEATURES

• Change the evaluation method: now compute the balanced classification rate.

biosigner 0.3.6

NEW FEATURES

• unit tests added

biosigner 0.3.5

SIGNIFICANT USER-VISIBLE CHANGES

• 'diagnosign' 'randomforest' method now available

biosigner 0.3.4

NEW FEATURES

• Galaxy module for rdiagnosign has been developed
• ggplot2 removed from dependencies (since it is not used currently)

biosigner 0.3.3

SIGNIFICANT USER-VISIBLE CHANGES

• renaming some of the 'dignosign' arguments for simplicity crossValI -> crossvalI nbootI -> bootI permutationI -> permI pvalThreshN -> pvalN

biosigner 0.3.2

NEW FEATURES

• bootstraping included into 'diagnosign' (instead of cross-validation)

biosigner 0.3.1

SIGNIFICANT USER-VISIBLE CHANGES

• package renamed: 'rdiagnosign' (instead of 'multimark') class 'diagnosign' methods 'diagnosign', 'print.diagnosign', 'plot.diagnosign'

biosigner 0.2.3

NEW FEATURES

• internal parameter 'alpha' set to 0.05 instead of 0

biosigner 0.2.2

SIGNIFICANT USER-VISIBLE CHANGES

• 'signastic' function (replaces 'fsi'): to compute significant features and corresponding models

biosigner 0.2.1

SIGNIFICANT USER-VISIBLE CHANGES

• rename data set tables proMN -> dataMatrix obsDF -> sampleMetadata feaDF -> variableMetadata

biosigner 0.2.0

NEW FEATURES

• 'pls' method available (in addition to 'svm')