Changes in version 0.99.9                        

BUG FIXES

    o   The CITATION file has been removde.

                       Changes in version 0.99.8                        

BUG FIXES

    o   The CITATION file can now be read with utils::readCitationFile() 
	even when the package metadata is not provided and the package is not 
	installed. In that case, fixed citation information is used instead 
	of the information from the installed package, which could be missing 
	or outdated

                       Changes in version 0.99.7                        

BUG FIXES

    o   The CITATION file can now be read with utils::readCitationFile() 
	when the package metadata is not provided. In that case, the 
	information is extracted from the installed package

                       Changes in version 0.99.6                        

BUG FIXES

    o   runSubtypingBimodal() no longer prints the number of iterations of 
	the mixtools::normalmixEM() function. A warning is now returned when 
	the mixture model does not converge for a signature

                       Changes in version 0.99.5                        

SIGNIFICANT USER-VISIBLE CHANGES

    o   Printing a SplitTypeRdata object, either by typing its name or with 
	print(), now displays a summary of the object (signatures, number of 
	samples, completed steps and number of samples assigned to each 
	signature) instead of the classification of each sample. The 
	classification of each sample is available with classification()

NEW FEATURES

    o   New show() method for the SplitTypeRdata class, which replaces the 
	print() method

                       Changes in version 0.99.4                        

NEW FEATURES

    o   New built-in signatures 'Miyabayashi_Fast' (231 genes) and 
	'Miyabayashi_Slow' (333 genes) from Miyabayashi et al. (2020). The gene 
	names have been updated from the Ensembl IDs (GENCODE v48 and 
	org.Hs.eg.db)

DOCUMENTATION

    o   The Description field of the DESCRIPTION file now describes the 
	classification method

    o   The Lustgarten Foundation has been added as funder and 
	'GeneSetEnrichment' has been added to the biocViews

                       Changes in version 0.99.3                        

SIGNIFICANT USER-VISIBLE CHANGES

    o   The built-in signatures have been renamed: 
	'2018_Tiriac_PDAC_PDO_basal-like_signature' is now 
	'Tiriac_PDAC_PDO_Basal_like' and 
	'2018_Tiriac_PDAC_PDO_classical_signature' is now 
	'Tiriac_PDAC_PDO_Classical'

    o   The signatures of the 'signaturesDemo' dataset have been renamed 
	'Classical' and 'Basal-like'

NEW FEATURES

    o   New built-in signatures 'Moffitt_Basal_like' and 'Moffitt_Classical' 
	from Moffitt et al. (2015)

    o   New CITATION file; citation("splitTypeR") now returns the package 
	citation

DOCUMENTATION

    o   Add or complete the examples of the SplitTypeRdata setter functions

    o   Add titles, descriptions and sources to the help pages of the 
	'signaturesDemo' and 'expNormalCountsDemo' datasets. The 
	'expNormalCountsDemo' dataset is described as simulated data

    o   New inst/scripts/README.md describing how the files in inst/extdata 
	were generated

    o   Vignette: new schematic figure for the classification step, new table 
	describing the runSubtypingBimodal() parameters, display of the full 
	mixture model and of the classification thresholds, and new scatter plot 
	comparing the classification with Tiriac et al. (2018)

                       Changes in version 0.99.2                        

NEW FEATURES

    o   New 'threshold' slot in the SplitTypeRdata class, with its 
	threshold() getter and setter. The slot contains the classification 
	threshold of each signature (the 95th percentile of the "low-mean" 
	distribution) and is filled by runSubtypingBimodal()

BUG FIXES

    o   The x-axis label of plotDensityWithUpscalingSamplesBimodal() is now 
	"GSVA score" instead of "GSEA score"

    o   plotDensityWithUpscalingSamplesBimodal() now restores the user's 
	graphical parameters (par()) on exit and returns NULL invisibly

                       Changes in version 0.99.1                        

BUG FIXES

    o   The validation of the 'permNbr' and 'upscaleNbr' parameters now 
	correctly rejects integer values below the minimum (ex: 2L, 0L) and 
	non-whole numbers (ex: 5.5)

                       Changes in version 0.99.0                        

NEW FEATURES

    o   Package creation