SeqMiner                Efficiently Read Sequencing Data (VCF format,
                        METAL format) into R
[.PlinkFile             Read a gene from BGEN file and return a
                        genotype matrix
addJob                  Add a job to a workflow
annotateGene            Annotate a test variant
annotatePlain           Annotate a plain text file
annotateVcf             Annotate a VCF file
download.annotation.resource
                        Download annotation resources to a directory
getCovPair              Extract pair of positions by ranges
getRefBase              Annotate a test variant
isDirWritable           Test whether directory is writable
isInRange               Test whether a vector of positions are inside
                        given ranges
isTabixRange            Check if the inputs are valid tabix range such
                        as chr1:2-300
makeAnnotationParameter
                        Construct a usable set of annotation parameters
newJob                  Create a new job
newWorkflow             Create a new workflow
openPlink               Open binary PLINK files
readBGENToListByGene    Read information from BGEN file in a given
                        range and return a list
readBGENToListByRange   Read information from BGEN file in a given
                        range and return a list
readBGENToMatrixByGene
                        Read a gene from BGEN file and return a
                        genotype matrix
readBGENToMatrixByRange
                        Read a gene from BGEN file and return a
                        genotype matrix
readPlinkToMatrixByIndex
                        Read a gene from BGEN file and return a
                        genotype matrix
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 genotype
                        matrix
readVCFToMatrixByRange
                        Read a gene from VCF file and return a genotype
                        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
verifyFilename          validate the inVcf can be created, and outVcf
                        can be write to. will stop if any error occurs
writeWorkflow           Export workflow to Makefile
