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.

AuthorXiaowei 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 publication2017-01-13 13:08:08
MaintainerXiaowei Zhan <zhanxw@gmail.com>
LicenseGPL | file LICENSE
Version5.7
http://seqminer.genomic.codes

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

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