Man pages for seqminer
Efficiently Read Sequence Data (VCF Format, BCF Format and METAL Format) into R

addJobAdd a job to a workflow
annotateGeneAnnotate a test variant
annotatePlainAnnotate a plain text file
annotateVcfAnnotate a VCF file
download.annotation.resourceDownload annotation resources to a directory
getCovPairExtract pair of positions by ranges
getRefBaseAnnotate a test variant
hasIndexCheck input file has tabix index
isDirWritableTest whether directory is writable
isInRangeTest whether a vector of positions are inside given ranges
isTabixRangeCheck if the inputs are valid tabix range such as chr1:2-300
isURLCheck if the input is url e.g. http:// or ftp://
makeAnnotationParameterConstruct a usable set of annotation parameters
newJobCreate a new job
newWorkflowCreate a new workflow
readVCFToListByGeneRead information from VCF file in a given range and return a...
readVCFToListByRangeRead information from VCF file in a given range and return a...
readVCFToMatrixByGeneRead a gene from VCF file and return a genotype matrix
readVCFToMatrixByRangeRead a gene from VCF file and return a genotype matrix
rvmeta.readCovByRangeRead covariance by range from METAL-format files.
rvmeta.readDataByGeneRead association statistics by gene from METAL-format files....
rvmeta.readDataByRangeRead association statistics by range from METAL-format files....
rvmeta.readNullModelRead null model statistics
rvmeta.readScoreByRangeRead score test statistics by range from METAL-format files.
rvmeta.readSkewByRangeRead skew by range from METAL-format files.
rvmeta.writeCovDataWrite covariance association statistics files.
rvmeta.writeScoreDataWrite score-based association statistics files.
SeqMinerEfficiently Read Sequencing Data (VCF format, METAL format)...
tabix.createIndexCreate tabix index file, similar to running tabix in command...
tabix.createIndex.metaCreate tabix index for bgzipped MetaScore/MetaCov file
tabix.createIndex.vcfCreate tabix index for bgzipped VCF file
tabix.readRead tabix file, similar to running tabix in command line.
tabix.read.headerRead tabix file, similar to running tabix in command line.
tabix.read.tableRead tabix file, similar to running tabix in command line.
validateAnnotationParameterValidate annotate parameter is valid
verifyFilenamevalidate the inVcf can be created, and outVcf can be write...
writeWorkflowExport workflow to Makefile
seqminer documentation built on Aug. 4, 2018, 5:05 p.m.