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.

Author
Xiuwen Zheng [aut, cre], Stephanie Gogarten [aut], David Levine [ctb], Cathy Laurie [ctb]
Date of publication
None
Maintainer
Xiuwen Zheng <zhengx@u.washington.edu>
License
GPL-3
Version
1.14.0
URLs

View on Bioconductor

Man pages

KG_P1_SampData
Simulated sample data for 1000 Genomes Phase 1
seqAlleleFreq
Get Allele Frequencies or Counts
seqApply
Apply Functions Over Array Margins
SeqArray-package
Big Data Management of Whole-Genome Sequence Variant Calls
seqBED2GDS
Convert PLINK BED Format to SeqArray Format
seqBlockApply
Apply Functions Over Array Margins via Blocking
seqClose
Close the SeqArray GDS File
seqDelete
Delete GDS Variables
seqDigest
Hash function digests
seqExampleFileName
Example files
seqExport
Export to a GDS File
seqGDS2SNP
Convert to a SNP GDS File
seqGDS2VCF
Convert to a VCF File
seqGetData
Get Data
seqGetFilter
Get the Filter of GDS File
seqMerge
Merge Multiple SeqArray GDS Files
seqMissing
Missing genotype percentage
seqNumAllele
Number of alleles
seqOpen
Open a SeqArray GDS File
seqOptimize
Optimize the Storage of Data Array
seqParallel
Apply Functions in Parallel
seqParallelSetup
Setup/Get a Parallel Environment
seqSetFilter
Set a Filter to Sample or Variant
seqSNP2GDS
Convert SNPRelate Format to SeqArray Format
seqStorageOption
Storage and Compression Options
seqSummary
Summarize a SeqArray GDS File
seqSystem
Get the parameters in the GDS system
seqTranspose
Transpose Data Array
SeqVarGDSClass-class
SeqVarGDSClass
seqVCF2GDS
Reformat VCF Files
seqVCF_Header
Parse the Header of a VCF File
seqVCF_SampID
Get the Sample IDs

Files in this package

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