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

Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R.

Author
Xiaowei Zhan [aut, cre], Dajiang Liu [aut], Attractive Chaos [cph] (We have used the following software and made minimal necessary changes: Tabix, Heng Li <lh3@live.co.uk> (MIT license). We removed standard IO related functions, e.g. printf, fprintf ; also changed its un-safe pointer arithmetics.), Broad Institute / Massachusetts Institute of Technology [cph], Genome Research Ltd (GRL) [cph]
Date of publication
2016-05-07 09:00:05
Maintainer
Xiaowei Zhan <zhanxw@gmail.com>
License
GPL | file LICENSE
Version
5.3
URLs

View on CRAN

Man pages

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
hasIndex
Check input file has tabix index
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
isURL
Check if the input is url e.g. http:// or ftp://
makeAnnotationParameter
Construct a usable set of annotation parameters
newJob
Create a new job
newWorkflow
Create a new workflow
readVCFToListByGene
Read information from VCF file in a given range and return a...
readVCFToListByRange
Read information from VCF file in a given range and return a...
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....
rvmeta.readDataByRange
Read association statistics by range from METAL-format files....
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)...
tabix.createIndex
Create tabix index file, similar to running tabix in command...
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...
writeWorkflow
Export workflow to Makefile

Files in this package

seqminer
seqminer/inst
seqminer/inst/CITATION
seqminer/inst/vcf
seqminer/inst/vcf/all.anno.filtered.extract.bcf.gz
seqminer/inst/vcf/all.anno.filtered.extract.vcf.gz.tbi
seqminer/inst/vcf/all.anno.filtered.extract.vcf.gz
seqminer/inst/vcf/all.anno.filtered.extract.bcf.gz.bci
seqminer/inst/vcf/1000g.phase1.20110521.CFH.var.anno.vcf.gz
seqminer/inst/vcf/refFlat_hg19_6col.txt.gz
seqminer/inst/vcf/1000g.phase1.20110521.CFH.var.anno.vcf.gz.tbi
seqminer/inst/tests
seqminer/inst/tests/testthat.R
seqminer/inst/tests/correct.Rdata
seqminer/inst/rvtests
seqminer/inst/rvtests/rvtest.MetaSkew.assoc.gz
seqminer/inst/rvtests/rvtest.MetaCov.assoc.gz.tbi
seqminer/inst/rvtests/rvtest.MetaScore.assoc.anno.gz.tbi
seqminer/inst/rvtests/rvtest.MetaSkew.assoc.gz.tbi
seqminer/inst/rvtests/rvtest.MetaScore.assoc.gz
seqminer/inst/rvtests/rvtest.MetaScore.assoc.anno.gz
seqminer/inst/rvtests/rvtest.MetaScore.assoc.gz.tbi
seqminer/inst/rvtests/cfh.refFlat.txt
seqminer/inst/rvtests/rvtest.MetaCov.assoc.gz
seqminer/inst/doc
seqminer/inst/doc/Manual.html
seqminer/inst/tabanno
seqminer/inst/tabanno/test.dbNSFP.gz.tbi
seqminer/inst/tabanno/input.demo.vcf
seqminer/inst/tabanno/input.100.vcf.gz
seqminer/inst/tabanno/test.bed
seqminer/inst/tabanno/test.fa.fai
seqminer/inst/tabanno/test.gene.txt
seqminer/inst/tabanno/priority.epact.txt
seqminer/inst/tabanno/test.dbNSFP.gz
seqminer/inst/tabanno/input.test.vcf
seqminer/inst/tabanno/tmp.vcf
seqminer/inst/tabanno/priority.txt
seqminer/inst/tabanno/test.fa
seqminer/inst/tabanno/input.test.plain.txt
seqminer/inst/tabanno/codon.txt
seqminer/configure.ac
seqminer/tests
seqminer/tests/tests.R
seqminer/src
seqminer/src/bcfutils.c
seqminer/src/GenomeSequence.h
seqminer/src/RangeList.h
seqminer/src/SequenceUtil.h
seqminer/src/vcf.c
seqminer/src/bcf.h
seqminer/src/AnnotationOutput.h
seqminer/src/VCFUtil.h
seqminer/src/bam_endian.h
seqminer/src/bcf_index.c
seqminer/src/VCFConstant.h
seqminer/src/tabix_index.c
seqminer/src/Utils.h
seqminer/src/vcf2genoLoader.cpp
seqminer/src/TypeConversion.h
seqminer/src/StringTemplate.h
seqminer/src/SimpleMatrix.cpp
seqminer/src/kstring.c
seqminer/src/bgzf.c
seqminer/src/bcf.c
seqminer/src/FreqTable.h
seqminer/src/bgzf.h
seqminer/src/TypeConversion.cpp
seqminer/src/ksort.h
seqminer/src/VCFInputFile.h
seqminer/src/Gene.h
seqminer/src/Codon.h
seqminer/src/config.h.in
seqminer/src/R_CPP_interface.cpp
seqminer/src/TabixData.h
seqminer/src/VCFUtil.cpp
seqminer/src/knetfile.h
seqminer/src/BCFReader.h
seqminer/src/Common.h
seqminer/src/VCFInfo.cpp
seqminer/src/seqminer.c
seqminer/src/Range.h
seqminer/src/PeopleSet.cpp
seqminer/src/BCFReader.cpp
seqminer/src/Rannotation.h
seqminer/src/GeneAnnotation.h
seqminer/src/AnnotationController.h
seqminer/src/Priority.h
seqminer/src/HiCExtract.h
seqminer/src/RangeList.cpp
seqminer/src/VCFFunction.h
seqminer/src/R_CPP_interface.h
seqminer/src/VCFHeader.h
seqminer/src/PatternMatch.h
seqminer/src/seqForStat.c
seqminer/src/PatternMatch.cpp
seqminer/src/GeneLoader.h
seqminer/src/tabixLoader.cpp
seqminer/src/Profiler.cpp
seqminer/src/AnnotationOutputFile.h
seqminer/src/VCFExtractor.h
seqminer/src/VCFInputFile.cpp
seqminer/src/VCFValue.h
seqminer/src/rvMetaLoader.cpp
seqminer/src/tabix.h
seqminer/src/VCFFilter.h
seqminer/src/PlinkOutputFile.h
seqminer/src/AnnotationString.h
seqminer/src/GeneFormat.h
seqminer/src/Exception.h
seqminer/src/VCFHeader.cpp
seqminer/src/bedidx.c
seqminer/src/kseq.h
seqminer/src/IO.cpp
seqminer/src/Utils.cpp
seqminer/src/PeopleSet.h
seqminer/src/Makevars.in
seqminer/src/Type.h
seqminer/src/khash.h
seqminer/src/VCFRecord.h
seqminer/src/rvMetaLoader.h
seqminer/src/StringUtil.h
seqminer/src/Profiler.h
seqminer/src/Exception.cpp
seqminer/src/Maximum.h
seqminer/src/SimpleTimer.h
seqminer/src/knetfile.c
seqminer/src/PlinkInputFile.h
seqminer/src/SimpleMatrix.h
seqminer/src/AnnotationResultCollection.h
seqminer/src/BedReader.h
seqminer/src/LogFile.h
seqminer/src/FileFormat.h
seqminer/src/OrderedMap.h
seqminer/src/VCFBuffer.h
seqminer/src/Makevars.win
seqminer/src/PlinkOutputFile.cpp
seqminer/src/VCFInfo.h
seqminer/src/GeneLoader.cpp
seqminer/src/tabixLoader.h
seqminer/src/VCFIndividual.h
seqminer/src/GenomeScore.h
seqminer/src/VCFOutputFile.h
seqminer/src/kstring.h
seqminer/src/Rannotation.cpp
seqminer/src/VCFIndividual.cpp
seqminer/src/vcf2genoLoader.h
seqminer/src/PlinkInputFile.cpp
seqminer/src/AnnotationResult.h
seqminer/src/AnnotationInputFile.h
seqminer/src/ModelParser.h
seqminer/src/IO.h
seqminer/src/TabixReader.h
seqminer/NAMESPACE
seqminer/demo
seqminer/demo/meta.workflow.R
seqminer/demo/vcf.workflow.R
seqminer/demo/00Index
seqminer/demo/annotate.R
seqminer/R
seqminer/R/genMakefile.R
seqminer/R/seqminer.R
seqminer/README.md
seqminer/MD5
seqminer/DESCRIPTION
seqminer/configure
seqminer/ChangeLog
seqminer/man
seqminer/man/readVCFToMatrixByRange.Rd
seqminer/man/tabix.createIndex.vcf.Rd
seqminer/man/readVCFToListByGene.Rd
seqminer/man/tabix.createIndex.meta.Rd
seqminer/man/rvmeta.readSkewByRange.Rd
seqminer/man/newJob.Rd
seqminer/man/getRefBase.Rd
seqminer/man/readVCFToListByRange.Rd
seqminer/man/writeWorkflow.Rd
seqminer/man/verifyFilename.Rd
seqminer/man/isDirWritable.Rd
seqminer/man/annotateGene.Rd
seqminer/man/tabix.read.header.Rd
seqminer/man/tabix.createIndex.Rd
seqminer/man/rvmeta.readNullModel.Rd
seqminer/man/tabix.read.table.Rd
seqminer/man/annotatePlain.Rd
seqminer/man/addJob.Rd
seqminer/man/download.annotation.resource.Rd
seqminer/man/rvmeta.writeScoreData.Rd
seqminer/man/getCovPair.Rd
seqminer/man/isInRange.Rd
seqminer/man/rvmeta.readCovByRange.Rd
seqminer/man/annotateVcf.Rd
seqminer/man/SeqMiner.Rd
seqminer/man/hasIndex.Rd
seqminer/man/tabix.read.Rd
seqminer/man/isTabixRange.Rd
seqminer/man/rvmeta.readDataByRange.Rd
seqminer/man/rvmeta.readScoreByRange.Rd
seqminer/man/rvmeta.writeCovData.Rd
seqminer/man/newWorkflow.Rd
seqminer/man/isURL.Rd
seqminer/man/validateAnnotationParameter.Rd
seqminer/man/readVCFToMatrixByGene.Rd
seqminer/man/makeAnnotationParameter.Rd
seqminer/man/rvmeta.readDataByGene.Rd
seqminer/configure.win
seqminer/cleanup
seqminer/LICENSE