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

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Documentation for package ‘seqminer’ version 9.4

• 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