CHANGES IN VERSION 1.3.0 ------------------------ NEW FEATURES o summarizeVariants() for summarizing counts by sample o new VariantType promoterVariants() added to locateVariants() MODIFICATIONS o ref(), alt(), filt() and qual() accessors for VCF-class now return a single variable instead of GRanges with variable as metadata CHANGES IN VERSION 1.2.0 ------------------------ NEW FEATURES o readVcf() has genome argument, can be subset on ranges or VCF elements with ScanVcfParam() o scanVcfHeader() returns VCFHeader class with accessors fixed, info, geno, etc. o writeVcf() writes out a VCF file from a VCF class o locateVariants() - returns GRanges instead of DataFrame - 'region' argument allows specification of variants by region - output includes txID, geneID and cdsID - has cache argument for repeated calls over multiple vcf files o predictCoding() - returns GRanges instead of DataFrame - output includes txID, geneID, cdsID, cds-based and protein-based coordinates CHANGES IN VERSION 1.0.0 ------------------------ NEW FEATURES o readVcf() for reading and parsing VCF files into a SummarizedExperiment o locateVariants() and predictCoding() for identifying amino acid coding changes in nonsynonymous variants o dbSNPFilter() and regionFilter() for filtering variants on membership in dbSNP or on a particular location in the genome o access to PolyPhen and SIFT predictions through keys() , cols() and select() methods. See ?SIFT or ?PolyPhen. BUG FIXES o No changes classified as 'bug fixes' (package under active development)