SeqArray: Big Data Management of Whole-genome Sequence Variant Calls

Big data management of whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.

AuthorXiuwen Zheng [aut, cre], Stephanie Gogarten [aut], David Levine [ctb], Cathy Laurie [ctb]
Date of publicationNone
MaintainerXiuwen Zheng <zhengx@u.washington.edu>
LicenseGPL-3
Version1.14.1
http://github.com/zhengxwen/SeqArray

View on Bioconductor

Functions

alt,SeqVarGDSClass-method Man page
asVCF,SeqVarGDSClass-method Man page
colData,SeqVarGDSClass-method Man page
filt,SeqVarGDSClass-method Man page
fixed,SeqVarGDSClass-method Man page
geno,SeqVarGDSClass,ANY-method Man page
geno,SeqVarGDSClass-method Man page
granges,SeqVarGDSClass-method Man page
header,SeqVarGDSClass-method Man page
info,SeqVarGDSClass-method Man page
KG_P1_SampData Man page
qual,SeqVarGDSClass-method Man page
ref,SeqVarGDSClass-method Man page
rowRanges,SeqVarGDSClass-method Man page
seqAlleleCount Man page
seqAlleleFreq Man page
seqApply Man page
SeqArray Man page
SeqArray-package Man page
seqBED2GDS Man page
seqBlockApply Man page
seqClose Man page
seqClose,gds.class-method Man page
seqClose,SeqVarGDSClass-method Man page
seqDelete Man page
seqDigest Man page
seqExampleFileName Man page
seqExport Man page
seqGDS2SNP Man page
seqGDS2VCF Man page
seqGetData Man page
seqGetFilter Man page
seqGetParallel Man page
seqMerge Man page
seqMissing Man page
seqNumAllele Man page
seqOpen Man page
seqOptimize Man page
seqParallel Man page
seqParallelSetup Man page
seqParApply Man page
seqResetFilter Man page
seqSetFilter Man page
seqSetFilterChrom Man page
seqSetFilter,SeqVarGDSClass,ANY-method Man page
seqSetFilter,SeqVarGDSClass,GRangesList-method Man page
seqSetFilter,SeqVarGDSClass,GRanges-method Man page
seqSetFilter,SeqVarGDSClass,IRanges-method Man page
seqSNP2GDS Man page
seqStorageOption Man page
seqSummary Man page
seqSystem Man page
seqTranspose Man page
SeqVarGDSClass Man page
SeqVarGDSClass-class Man page
seqVCF2GDS Man page
seqVCF_Header Man page
seqVCF_SampID Man page

Files

SeqArray/DESCRIPTION
SeqArray/NAMESPACE
SeqArray/NEWS
SeqArray/R
SeqArray/R/AllClasses.R SeqArray/R/AllGenerics.R SeqArray/R/ConvVCF2GDS.R SeqArray/R/Conversion.R SeqArray/R/Internal.R SeqArray/R/Methods-SeqVarGDSClass.R SeqArray/R/Methods.R SeqArray/R/Summary.R SeqArray/R/Utilities.R SeqArray/R/UtilsExport.R SeqArray/R/UtilsMerge.R
SeqArray/README.md
SeqArray/TODO
SeqArray/build
SeqArray/build/vignette.rds
SeqArray/data
SeqArray/data/KG_P1_SampData.RData
SeqArray/inst
SeqArray/inst/doc
SeqArray/inst/doc/OverviewSlides.Rmd
SeqArray/inst/doc/OverviewSlides.html
SeqArray/inst/doc/R_Integration.R
SeqArray/inst/doc/R_Integration.Rmd
SeqArray/inst/doc/R_Integration.html
SeqArray/inst/doc/SeqArrayTutorial.R
SeqArray/inst/doc/SeqArrayTutorial.Rmd
SeqArray/inst/doc/SeqArrayTutorial.html
SeqArray/inst/extdata
SeqArray/inst/extdata/1KG_phase1_release_v3_chr22.gds
SeqArray/inst/extdata/CEU_Exon.gds
SeqArray/inst/extdata/CEU_Exon.vcf.gz
SeqArray/inst/unitTests
SeqArray/inst/unitTests/data
SeqArray/inst/unitTests/data/Valid.RData
SeqArray/inst/unitTests/test_asVCF.R
SeqArray/inst/unitTests/test_c.R
SeqArray/inst/unitTests/test_cpp.R
SeqArray/inst/unitTests/test_examples.R
SeqArray/inst/unitTests/test_func.R
SeqArray/inst/unitTests/test_utils.R
SeqArray/man
SeqArray/man/KG_P1_SampData.Rd SeqArray/man/SeqArray-package.Rd SeqArray/man/SeqVarGDSClass-class.Rd SeqArray/man/seqAlleleFreq.Rd SeqArray/man/seqApply.Rd SeqArray/man/seqBED2GDS.Rd SeqArray/man/seqBlockApply.Rd SeqArray/man/seqClose.Rd SeqArray/man/seqDelete.Rd SeqArray/man/seqDigest.Rd SeqArray/man/seqExampleFileName.Rd SeqArray/man/seqExport.Rd SeqArray/man/seqGDS2SNP.Rd SeqArray/man/seqGDS2VCF.Rd SeqArray/man/seqGetData.Rd SeqArray/man/seqGetFilter.Rd SeqArray/man/seqMerge.Rd SeqArray/man/seqMissing.Rd SeqArray/man/seqNumAllele.Rd SeqArray/man/seqOpen.Rd SeqArray/man/seqOptimize.Rd SeqArray/man/seqParallel.Rd SeqArray/man/seqParallelSetup.Rd SeqArray/man/seqSNP2GDS.Rd SeqArray/man/seqSetFilter.Rd SeqArray/man/seqStorageOption.Rd SeqArray/man/seqSummary.Rd SeqArray/man/seqSystem.Rd SeqArray/man/seqTranspose.Rd SeqArray/man/seqVCF2GDS.Rd SeqArray/man/seqVCF_Header.Rd SeqArray/man/seqVCF_SampID.Rd
SeqArray/src
SeqArray/src/ConvGDS2VCF.cpp
SeqArray/src/ConvToGDS.cpp
SeqArray/src/ConvVCF2GDS.cpp
SeqArray/src/FileMerge.cpp
SeqArray/src/GetData.cpp
SeqArray/src/Index.cpp
SeqArray/src/Index.h
SeqArray/src/LinkSNPRelate.cpp
SeqArray/src/Makevars
SeqArray/src/Methods.cpp
SeqArray/src/R_SeqArray.c
SeqArray/src/ReadBySample.cpp
SeqArray/src/ReadBySample.h
SeqArray/src/ReadByVariant.cpp
SeqArray/src/ReadByVariant.h
SeqArray/src/SeqArray.cpp
SeqArray/src/pkg_test.cpp
SeqArray/src/vectorization.c
SeqArray/src/vectorization.h
SeqArray/tests
SeqArray/tests/test.R
SeqArray/vignettes
SeqArray/vignettes/OverviewSlides.Rmd
SeqArray/vignettes/R_Integration.Rmd
SeqArray/vignettes/SeqArrayTutorial.Rmd
SeqArray/vignettes/link.png
SeqArray/vignettes/seqarray_bib.bib
SeqArray/vignettes/seqarray_workflow.png

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