NEWS

splitTypeR 0.99.9

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fixed citation information is used instead of the information from the installed package, which could be missing or outdated

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

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

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

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)

The Description field of the DESCRIPTION file now describes the classification method
The Lustgarten Foundation has been added as funder and 'GeneSetEnrichment' has been added to the biocViews

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

New built-in signatures 'Moffitt_Basal_like' and 'Moffitt_Classical' from Moffitt et al. (2015)
New CITATION file; citation("splitTypeR") now returns the package citation

Add or complete the examples of the SplitTypeRdata setter functions
Add titles, descriptions and sources to the help pages of the 'signaturesDemo' and 'expNormalCountsDemo' datasets. The 'expNormalCountsDemo' dataset is described as simulated data
New inst/scripts/README.md describing how the files in inst/extdata were generated
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)

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()

The x-axis label of plotDensityWithUpscalingSamplesBimodal() is now "GSVA score" instead of "GSEA score"
plotDensityWithUpscalingSamplesBimodal() now restores the user's graphical parameters (par()) on exit and returns NULL invisibly

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)