NEWS

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TMSig 0.99.3 (2024-10-17)

MINOR CHANGES

• Addressed 'Consider shorter lines' NOTE from BiocCheck.

TMSig 0.99.2 (2024-10-17)

MINOR CHANGES

• Reduced size of TMSig vignette.

TMSig 0.99.1 (2024-09-30)

SIGNIFICANT USER-VISIBLE CHANGES

• Renamed functions to adhere to Bioconductor style: cluster_sets to clusterSets, decompose_sets to decomposeSets, filter_sets to filterSets, gmt_to_list to readGMT, incidence to sparseIncidence, incidence_to_list to incidenceToList, invert_sets to invertSets, range_extend to extendRangeNum, camera_color_fun to cameraColorFun, gsea_color_fun to gseaColorFun.
• Converted functions sparseIncidence, filterSets, and invertSets to S4 generics and add methods for objects of class GSEABase::GeneSet and GSEABase::GeneSetCollection. Added paragraph explaining how sparseIncidence differs from GSEABase::incidence.
• cameraPR.matrix(): added "ZScore" column to results (placed before "PValue" column). The default value of the statistic_column parameter of enrichmap was also updated to "ZScore".
• enrichmap(): heatmap rectangle fill and border color can now be changed via the heatmap_args parameter.
• enrichmap(): color legend title can now be changed via heatmap_args = list(name = "new title") instead of heatmap_args = list(heatmap_legend_param = list(title = "new title")).
• enrichmap(): added examples to documentation. Default text size is now controlled by the cell_size argument.
• enrichmap(): updated the heatmap layer function; all bubbles, regardless of significance, will have a radius of at least 0.2 * cell_size.

MINOR CHANGES

• Added inst/script/c5.go.v2023.2.Hs.symbols.txt file to describe the process used to generate c5.go.v2023.2.Hs.symbols.gmt.gz.

BUG FIXES

• Fixed manual build errors caused by special characters used in LaTeX equations.

TMSig 0.99.0 (2024-08-24)

• Initial version.