SeqMiner                Efficiently Read Sequencing Data (VCF format,
                        METAL format) into R
annotateGene            Annotate a test variant
annotatePlain           Annotate a plain text file
annotateVcf             Annotate a VCF file
getCovPair              Extract pair of positions by ranges
getRefBase              Annotate a test variant
isInRange               Test whether a vector of positions are inside
                        given ranges
makeAnnotationParameter
                        Construct a usable set of annotation parameters
readVCFToListByGene     Read information from VCF file in a given range
                        and return a list
readVCFToListByRange    Read information from VCF file in a given range
                        and return a list
readVCFToMatrixByGene   Read a gene from VCF file and return a
                        genotypes matrix
readVCFToMatrixByRange
                        Read a gene from VCF file and return a
                        genotypes matrix
rvmeta.readCovByRange   Read covariance by range from METAL-format
                        files.
rvmeta.readDataByGene   Read association statistics by gene from
                        METAL-format files. Both score statistics and
                        covariance statistics will be extracted.
rvmeta.readDataByRange
                        Read association statistics by range from
                        METAL-format files. Both score statistics and
                        covariance statistics will be extracted.
rvmeta.readNullModel    Read null model statistics
rvmeta.readScoreByRange
                        Read score test statistics by range from
                        METAL-format files.
rvmeta.readSkewByRange
                        Read skew by range from METAL-format files.
rvmeta.writeCovData     Write covariance association statistics files.
rvmeta.writeScoreData   Write score-based association statistics files.
tabix.createIndex       Create tabix index file, similar to running
                        tabix in command line.
tabix.createIndex.meta
                        Create tabix index for bgzipped
                        MetaScore/MetaCov file
tabix.createIndex.vcf   Create tabix index for bgzipped VCF file
tabix.read              Read tabix file, similar to running tabix in
                        command line.
tabix.read.header       Read tabix file, similar to running tabix in
                        command line.
tabix.read.table        Read tabix file, similar to running tabix in
                        command line.
validateAnnotationParameter
                        Validate annotate parameter is valid
