# Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

## Documentation for package ‘seqminer’ version 9.9

- DESCRIPTION file.
- Code demos. Use demo() to run them.

## Help Pages

seqminer-package | Efficiently Read Sequencing Data (VCF format, METAL format) into R
addJob | Add a job to a workflow
annotateGene | Annotate a test variant
annotatePlain | Annotate a plain text file
annotateVcf | Annotate a VCF file
createSingleChromosomeBCFIndex | Create a single chromosome index
createSingleChromosomeVCFIndex | Create a single chromosome index
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 from binary PLINK file and return a genotype matrix
readSingleChromosomeBCFToMatrixByRange | Read a range from BCF file and return a genotype matrix
readSingleChromosomeVCFToMatrixByRange | Read a range from VCF 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.
seqminer | Efficiently Read Sequencing Data (VCF format, METAL format) into R
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
[.PlinkFile | Read from binary PLINK file and return a genotype matrix