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

Functions

addJob Man page
annotateGene Man page
annotatePlain Man page
annotateVcf Man page
download.annotation.resource Man page
getCovPair Man page
getRefBase Man page
hasIndex Man page
isDirWritable Man page
isInRange Man page
isTabixRange Man page
isURL Man page
makeAnnotationParameter Man page
newJob Man page
newWorkflow Man page
readVCFToListByGene Man page
readVCFToListByRange Man page
readVCFToMatrixByGene Man page
readVCFToMatrixByRange Man page
rvmeta.readCovByRange Man page
rvmeta.readDataByGene Man page
rvmeta.readDataByRange Man page
rvmeta.readNullModel Man page
rvmeta.readScoreByRange Man page
rvmeta.readSkewByRange Man page
rvmeta.writeCovData Man page
rvmeta.writeScoreData Man page
SeqMiner Man page
SeqMiner-package Man page
tabix.createIndex Man page
tabix.createIndex.meta Man page
tabix.createIndex.vcf Man page
tabix.read Man page
tabix.read.header Man page
tabix.read.table Man page
validateAnnotationParameter Man page
verifyFilename Man page
writeWorkflow Man page

Files

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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