SeqArray: Big Data Management of Whole-genome Sequence Variant Calls
Version 1.16.0

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]
Bioconductor views DataRepresentation Genetics Infrastructure Sequencing
Date of publicationNone
MaintainerXiuwen Zheng <zhengx@u.washington.edu>
LicenseGPL-3
Version1.16.0
URL http://github.com/zhengxwen/SeqArray
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SeqArray")

Getting started

Package overview
README.md
Integration with R
SeqArray Data Format and Access
SeqArray Overview

Popular man pages

seqClose: Close the SeqArray GDS File
seqExampleFileName: Example files
seqGDS2SNP: Convert to a SNP GDS File
seqGDS2VCF: Convert to a VCF File
seqOptimize: Optimize the Storage of Data Array
seqParallel: Apply Functions in Parallel
seqSetFilterCond: Set a Filter to Variant with Allele Count/Freq
See all...

All man pages Function index File listing

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
seqSetFilterCond: Set a Filter to Variant with Allele Count/Freq
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

Functions

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/ConvVCF2GDS.R
R/Conversion.R
R/Internal.R
R/Methods-SeqVarGDSClass.R
R/Methods.R
R/Summary.R
R/Utilities.R
R/UtilsExport.R
R/UtilsMerge.R
README.md
TODO
build
build/vignette.rds
data
data/KG_P1_SampData.RData
inst
inst/CITATION
inst/doc
inst/doc/OverviewSlides.Rmd
inst/doc/OverviewSlides.html
inst/doc/R_Integration.R
inst/doc/R_Integration.Rmd
inst/doc/R_Integration.html
inst/doc/SeqArrayTutorial.R
inst/doc/SeqArrayTutorial.Rmd
inst/doc/SeqArrayTutorial.html
inst/extdata
inst/extdata/1KG_phase1_release_v3_chr22.gds
inst/extdata/CEU_Exon.gds
inst/extdata/CEU_Exon.vcf.gz
inst/unitTests
inst/unitTests/data
inst/unitTests/data/Valid.RData
inst/unitTests/test_asVCF.R
inst/unitTests/test_c.R
inst/unitTests/test_cpp.R
inst/unitTests/test_examples.R
inst/unitTests/test_func.R
inst/unitTests/test_utils.R
man
man/KG_P1_SampData.Rd
man/SeqArray-package.Rd
man/SeqVarGDSClass-class.Rd
man/seqAlleleFreq.Rd
man/seqApply.Rd
man/seqBED2GDS.Rd
man/seqBlockApply.Rd
man/seqClose.Rd
man/seqDelete.Rd
man/seqDigest.Rd
man/seqExampleFileName.Rd
man/seqExport.Rd
man/seqGDS2SNP.Rd
man/seqGDS2VCF.Rd
man/seqGetData.Rd
man/seqGetFilter.Rd
man/seqMerge.Rd
man/seqMissing.Rd
man/seqNumAllele.Rd
man/seqOpen.Rd
man/seqOptimize.Rd
man/seqParallel.Rd
man/seqParallelSetup.Rd
man/seqSNP2GDS.Rd
man/seqSetFilter.Rd
man/seqSetFilterCond.Rd
man/seqStorageOption.Rd
man/seqSummary.Rd
man/seqSystem.Rd
man/seqTranspose.Rd
man/seqVCF2GDS.Rd
man/seqVCF_Header.Rd
man/seqVCF_SampID.Rd
src
src/ConvGDS2VCF.cpp
src/ConvToGDS.cpp
src/ConvVCF2GDS.cpp
src/FileMerge.cpp
src/GetData.cpp
src/Index.cpp
src/Index.h
src/LinkSNPRelate.cpp
src/Makevars
src/Methods.cpp
src/R_SeqArray.c
src/ReadBySample.cpp
src/ReadBySample.h
src/ReadByVariant.cpp
src/ReadByVariant.h
src/SeqArray.cpp
src/pkg_test.cpp
src/vectorization.c
src/vectorization.h
tests
tests/test.R
vignettes
vignettes/OverviewSlides.Rmd
vignettes/R_Integration.Rmd
vignettes/SeqArrayTutorial.Rmd
vignettes/link.png
vignettes/seqarray_bib.bib
vignettes/seqarray_workflow.png
SeqArray documentation built on May 20, 2017, 9:33 p.m.

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