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

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Documentation for package ‘seqminer’ version 3.4

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SeqMiner-package 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.
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