CHANGES IN VERSION 1.4.00
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NEW FUNCTIONS
    o plotApobecDiff - plots differences between APOBEC enriched and non APOBEC enriched samples
    o gisticOncoplot, gisticBubblePlot and gisticChromPlot to visualize GISTIC results
    o somaticInteractions - to identify mutually exclusive/co-occuring gene sets
    o genotypeMatrix - function to create genotype matrix
    o mutCountMatrix - generate count matrix

SIGNIFICANT USER-LEVEL IMPROVEMENT
    o Changes to MAF object: It now includes clinical data slot similar to PhenoData of expressionset objects.
    o Changes to MAF object: Silent variants will be stored seperately in MAF object and won't be mixed with non-syn variants.
    o Changes to MAF object: Oncomatrix is built on the fly whenever required, its no longer stored in MAF object.
    o You can specify a manual list of variant classifications to be considered as non-synonymous via argument vc_nonSyn in read.maf
    o Dropped mutExclusive function - Use somaticInteractions instead.
    o Many sorting options and plotting improvements to oncplots.
    o One can include q values from mutsig (or any similar program) as a side barplot in oncoplot
    o rainfallPlot can detect hyper mutated genomic segments via ChangePoint detection method
    o plotSignatures includes cosine similarity score and aetiology of detected signature
    o readGistic has argument cnLevel to choose deep or shallow CN variants
    o inferHeterogeneity includes MATH score in the plot
    o Tumor_Sample_Barcodes remains as is; earlier '-' were converted to '.' in sample names

NON SIGNIFICANT CHANGES
    o mafCompare output includes adjusted p-values
    o trinucleotideMatrix output includes adjusted p-values for APOBEC enrichment
    o added plot arguments to control title size and point size in lollipopPlot

BUG FIXES
    o Major bug fix in signature analysis
    o minor bug fixes in oncostrip
