seqminer: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL Format) into R
Version 6.0

Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.

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 publication2017-05-05 17:42:58 UTC
MaintainerXiaowei Zhan <zhanxw@gmail.com>
LicenseGPL | file LICENSE
Version6.0
URL http://seqminer.genomic.codes
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("seqminer")

Getting started

README.md

Popular man pages

annotateVcf: Annotate a VCF file
getCovPair: Extract pair of positions by ranges
readVCFToMatrixByRange: Read a gene from VCF file and return a genotype matrix
tabix.createIndex.meta: Create tabix index for bgzipped MetaScore/MetaCov file
tabix.createIndex.vcf: Create tabix index for bgzipped VCF file
tabix.read.table: Read tabix file, similar to running tabix in command line.
writeWorkflow: Export workflow to Makefile
See all...

All man pages Function index File listing

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

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

Files

inst
inst/CITATION
inst/vcf
inst/vcf/all.anno.filtered.extract.bcf.gz
inst/vcf/all.anno.filtered.extract.vcf.gz.tbi
inst/vcf/all.anno.filtered.extract.vcf.gz
inst/vcf/all.anno.filtered.extract.bcf.gz.bci
inst/vcf/1000g.phase1.20110521.CFH.var.anno.vcf.gz
inst/vcf/refFlat_hg19_6col.txt.gz
inst/vcf/1000g.phase1.20110521.CFH.var.anno.vcf.gz.tbi
inst/tests
inst/tests/correct.Rdata
inst/rvtests
inst/rvtests/rvtest.MetaSkew.assoc.gz
inst/rvtests/rvtest.MetaCov.assoc.gz.tbi
inst/rvtests/rvtest.MetaScore.assoc.anno.gz.tbi
inst/rvtests/rvtest.MetaSkew.assoc.gz.tbi
inst/rvtests/rvtest.MetaScore.assoc.gz
inst/rvtests/rvtest.MetaScore.assoc.anno.gz
inst/rvtests/rvtest.MetaScore.assoc.gz.tbi
inst/rvtests/cfh.refFlat.txt
inst/rvtests/rvtest.MetaCov.assoc.gz
inst/doc
inst/doc/Manual.html
inst/tabanno
inst/tabanno/test.dbNSFP.gz.tbi
inst/tabanno/input.demo.vcf
inst/tabanno/input.100.vcf.gz
inst/tabanno/test.bed
inst/tabanno/test.fa.fai
inst/tabanno/test.gene.txt
inst/tabanno/priority.epact.txt
inst/tabanno/test.dbNSFP.gz
inst/tabanno/input.test.vcf
inst/tabanno/tmp.vcf
inst/tabanno/priority.txt
inst/tabanno/test.fa
inst/tabanno/input.test.plain.txt
inst/tabanno/codon.txt
inst/test-triallelic
inst/test-triallelic/test2.study3.MetaCov.assoc.gz
inst/test-triallelic/tri.MetaCov.assoc.gz
inst/test-triallelic/test2.study3.MetaScore.assoc.gz
inst/test-triallelic/bi.MetaScore.assoc.gz.tbi
inst/test-triallelic/bi.MetaCov.assoc.gz.tbi
inst/test-triallelic/test2.study3.MetaScore.assoc.gz.tbi
inst/test-triallelic/tri.MetaScore.assoc.gz.tbi
inst/test-triallelic/test2.study1.MetaCov.assoc.gz.tbi
inst/test-triallelic/test2.study3.MetaCov.assoc.gz.tbi
inst/test-triallelic/test2.study2.MetaCov.assoc.gz.tbi
inst/test-triallelic/bi.MetaCov.assoc.gz
inst/test-triallelic/test2.study1.MetaCov.assoc.gz
inst/test-triallelic/tri.MetaScore.assoc.gz
inst/test-triallelic/test2.study1.MetaScore.assoc.gz
inst/test-triallelic/test2.study2.MetaScore.assoc.gz.tbi
inst/test-triallelic/tri.MetaCov.assoc.gz.tbi
inst/test-triallelic/test2.study2.MetaScore.assoc.gz
inst/test-triallelic/test2.study2.MetaCov.assoc.gz
inst/test-triallelic/test2.study1.MetaScore.assoc.gz.tbi
inst/test-triallelic/bi.MetaScore.assoc.gz
configure.ac
tests
tests/testthat.R
tests/testthat
tests/testthat/test-triallelic.R
tests/testthat/test-vcf.R
src
src/bcfutils.c
src/GenomeSequence.h
src/RangeList.h
src/SequenceUtil.h
src/vcf.c
src/bcf.h
src/AnnotationOutput.h
src/VCFUtil.h
src/bam_endian.h
src/bcf_index.c
src/VCFConstant.h
src/tabix_index.c
src/Utils.h
src/vcf2genoLoader.cpp
src/TypeConversion.h
src/StringTemplate.h
src/SimpleMatrix.cpp
src/kstring.c
src/bgzf.c
src/bcf.c
src/FreqTable.h
src/bgzf.h
src/TypeConversion.cpp
src/ksort.h
src/VCFInputFile.h
src/Gene.h
src/Codon.h
src/config.h.in
src/R_CPP_interface.cpp
src/TabixData.h
src/VCFUtil.cpp
src/knetfile.h
src/BCFReader.h
src/Common.h
src/VCFInfo.cpp
src/seqminer.c
src/Range.h
src/PeopleSet.cpp
src/BCFReader.cpp
src/Rannotation.h
src/GeneAnnotation.h
src/AnnotationController.h
src/Priority.h
src/HiCExtract.h
src/RangeList.cpp
src/VCFFunction.h
src/R_CPP_interface.h
src/VCFHeader.h
src/PatternMatch.h
src/seqForStat.c
src/PatternMatch.cpp
src/GeneLoader.h
src/tabixLoader.cpp
src/Profiler.cpp
src/AnnotationOutputFile.h
src/VCFExtractor.h
src/VCFInputFile.cpp
src/VCFValue.h
src/rvMetaLoader.cpp
src/tabix.h
src/VCFFilter.h
src/PlinkOutputFile.h
src/AnnotationString.h
src/GeneFormat.h
src/Exception.h
src/VCFHeader.cpp
src/bedidx.c
src/kseq.h
src/IO.cpp
src/Utils.cpp
src/PeopleSet.h
src/Makevars.in
src/Type.h
src/seqminer_init.c
src/khash.h
src/VCFRecord.h
src/rvMetaLoader.h
src/StringUtil.h
src/Profiler.h
src/Exception.cpp
src/Maximum.h
src/SimpleTimer.h
src/knetfile.c
src/PlinkInputFile.h
src/SimpleMatrix.h
src/AnnotationResultCollection.h
src/BedReader.h
src/LogFile.h
src/FileFormat.h
src/OrderedMap.h
src/VCFBuffer.h
src/Makevars.win
src/PlinkOutputFile.cpp
src/VCFInfo.h
src/GeneLoader.cpp
src/tabixLoader.h
src/VCFIndividual.h
src/GenomeScore.h
src/VCFOutputFile.h
src/kstring.h
src/Rannotation.cpp
src/VCFIndividual.cpp
src/vcf2genoLoader.h
src/PlinkInputFile.cpp
src/AnnotationResult.h
src/AnnotationInputFile.h
src/ModelParser.h
src/IO.h
src/TabixReader.h
NAMESPACE
demo
demo/meta.workflow.R
demo/vcf.workflow.R
demo/00Index
demo/annotate.R
R
R/genMakefile.R
R/seqminer.R
README.md
MD5
DESCRIPTION
configure
ChangeLog
man
man/readVCFToMatrixByRange.Rd
man/tabix.createIndex.vcf.Rd
man/readVCFToListByGene.Rd
man/tabix.createIndex.meta.Rd
man/rvmeta.readSkewByRange.Rd
man/newJob.Rd
man/getRefBase.Rd
man/readVCFToListByRange.Rd
man/writeWorkflow.Rd
man/verifyFilename.Rd
man/isDirWritable.Rd
man/annotateGene.Rd
man/tabix.read.header.Rd
man/tabix.createIndex.Rd
man/rvmeta.readNullModel.Rd
man/tabix.read.table.Rd
man/annotatePlain.Rd
man/addJob.Rd
man/download.annotation.resource.Rd
man/rvmeta.writeScoreData.Rd
man/getCovPair.Rd
man/isInRange.Rd
man/rvmeta.readCovByRange.Rd
man/annotateVcf.Rd
man/SeqMiner.Rd
man/hasIndex.Rd
man/tabix.read.Rd
man/isTabixRange.Rd
man/rvmeta.readDataByRange.Rd
man/rvmeta.readScoreByRange.Rd
man/rvmeta.writeCovData.Rd
man/newWorkflow.Rd
man/isURL.Rd
man/validateAnnotationParameter.Rd
man/readVCFToMatrixByGene.Rd
man/makeAnnotationParameter.Rd
man/rvmeta.readDataByGene.Rd
configure.win
cleanup
LICENSE
seqminer documentation built on May 20, 2017, 12:19 a.m.