Package: SeqArray 1.47.0

Xiuwen Zheng

SeqArray: Data Management of Large-Scale Whole-Genome Sequence Variant Calls

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

Authors:Xiuwen Zheng [aut, cre], Stephanie Gogarten [aut], David Levine [ctb], Cathy Laurie [ctb]

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SeqArray.pdf |SeqArray.html✨
SeqArray/json (API)
NEWS

# Install 'SeqArray' in R:

install.packages('SeqArray', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zhengxwen/seqarray/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

KG_P1_SampData - Simulated sample data for 1000 Genomes Phase 1

On BioConductor:SeqArray-1.47.0(bioc 3.21)SeqArray-1.46.0(bioc 3.20)

infrastructure datarepresentation sequencing genetics bioinformatics gds-format snp snv wes wgs

12.01 score 43 stars 9 packages 1.1k scripts 1.6k downloads 8 mentions 70 exports 20 dependencies

Last updated 23 days agofrom:9bf676f480. Checks:OK: 1 NOTE: 3 WARNING: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win-x86_64	WARNING	Oct 31 2024
R-4.5-linux-x86_64	NOTE	Oct 31 2024
R-4.4-win-x86_64	WARNING	Oct 31 2024
R-4.4-mac-x86_64	WARNING	Oct 31 2024
R-4.4-mac-aarch64	NOTE	Oct 31 2024
R-4.3-win-x86_64	WARNING	Oct 31 2024
R-4.3-mac-x86_64	WARNING	Oct 31 2024
R-4.3-mac-aarch64	NOTE	Oct 31 2024

Exports:.Last.lib alt colData filt fixed geno granges header info qual ref rowRanges seqAddValue seqAlleleCount seqAlleleFreq seqApply seqAsVCF seqBCF2GDS seqBED2GDS seqBlockApply seqCheck seqClose seqDelete seqDigest seqEmptyFile seqExampleFileName seqExport seqFilterPop seqFilterPush seqGDS2BED seqGDS2SNP seqGDS2VCF seqGet2bGeno seqGetAF_AC_Missing seqGetData seqGetFilter seqGetParallel seqListVarData seqMerge seqMissing seqMulticoreSetup seqNewVarData seqNumAllele seqOpen seqOptimize seqParallel seqParallelSetup seqParApply seqRecompress seqResetFilter seqResetVariantID seqSetFilter seqSetFilterAnnotID seqSetFilterChrom seqSetFilterCond seqSetFilterPos seqSNP2GDS seqStorageOption seqSummary seqSystem seqTranspose seqUnitApply seqUnitCreate seqUnitFilterCond seqUnitMerge seqUnitSlidingWindows seqUnitSubset seqVCF_Header seqVCF_SampID seqVCF2GDS

Dependencies:askpass BiocGenerics Biostrings crayon curl gdsfmt GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite mime openssl R6 S4Vectors sys UCSC.utils XVector zlibbioc

Integration with R

Xiuwen Zheng (Department of Biostatistics, University of Washington, Seattle)

Rendered fromSeqArray.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2022-07-16
Started: 2019-10-22

SeqArray Data Format and Access

Xiuwen Zheng (Department of Biostatistics, University of Washington, Seattle)

Rendered fromSeqArrayTutorial.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2022-07-16
Started: 2015-06-14

SeqArray Overview

Dr. Xiuwen Zheng (Department of Biostatistics, University of Washington, Seattle)

Rendered fromOverviewSlides.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2022-07-16
Started: 2015-12-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Data Management of Large-scale Whole-Genome Sequence Variant Calls	SeqArray-package SeqArray
Simulated sample data for 1000 Genomes Phase 1	KG_P1_SampData
Add values to a GDS File	seqAddValue
Get Allele Frequencies or Counts	seqAlleleCount seqAlleleFreq seqGetAF_AC_Missing
Apply Functions Over Array Margins	seqApply
VariantAnnotation objects	seqAsVCF
Conversion between PLINK BED and SeqArray GDS	seqBED2GDS seqGDS2BED
Apply Functions Over Array Margins via Blocking	seqBlockApply
Data Integrity Checking	seqCheck
Close the SeqArray GDS File	seqClose seqClose,gds.class-method seqClose,SeqVarGDSClass-method
Delete GDS Variables	seqDelete
Hash function digests	seqDigest
Empty GDS file	seqEmptyFile
Example files	seqExampleFileName
Export to a GDS File	seqExport
Convert to a SNP GDS File	seqGDS2SNP
Convert to a VCF File	seqGDS2VCF
Get packed genotypes	seqGet2bGeno
Get Data	seqGetData
Get the Filter of GDS File	seqGetFilter
Merge Multiple SeqArray GDS Files	seqMerge
Missing genotype percentage	seqMissing
Variable-length data	seqListVarData seqNewVarData
Number of alleles	seqNumAllele
Open a SeqArray GDS File	seqOpen
Optimize the Storage of Data Array	seqOptimize
Apply Functions in Parallel	seqParallel seqParApply
Setup/Get a Parallel Environment	seqGetParallel seqMulticoreSetup seqParallelSetup
Recompress the GDS file	seqRecompress
Reset Variant ID in SeqArray GDS Files	seqResetVariantID
Set a Filter to Sample or Variant	seqFilterPop seqFilterPush seqResetFilter seqSetFilter seqSetFilter,SeqVarGDSClass,ANY-method seqSetFilter,SeqVarGDSClass,GRanges-method seqSetFilter,SeqVarGDSClass,GRangesList-method seqSetFilter,SeqVarGDSClass,IRanges-method seqSetFilterAnnotID seqSetFilterChrom seqSetFilterPos
Set a Filter to Variant with Allele Count/Freq	seqSetFilterCond
Convert SNPRelate Format to SeqArray Format	seqSNP2GDS
Storage and Compression Options	seqStorageOption
Summarize a SeqArray GDS File	seqSummary
Get the parameters in the GDS system	seqSystem
Transpose Data Array	seqTranspose
Apply Function Over Variant Units	seqUnitApply
Subset and merge the units	seqUnitCreate seqUnitMerge seqUnitSubset
Filter unit variants	seqUnitFilterCond
Sliding units of selected variants	seqUnitSlidingWindows
SeqVarGDSClass	alt alt,SeqVarGDSClass-method colData colData,SeqVarGDSClass-method filt filt,SeqVarGDSClass-method fixed fixed,SeqVarGDSClass-method geno geno,SeqVarGDSClass,ANY-method geno,SeqVarGDSClass-method granges,SeqVarGDSClass-method header header,SeqVarGDSClass-method info info,SeqVarGDSClass-method qual qual,SeqVarGDSClass-method ref ref,SeqVarGDSClass-method rowRanges rowRanges,SeqVarGDSClass-method SeqVarGDSClass SeqVarGDSClass-class
Parse the Header of a VCF/BCF File	seqVCF_Header
Get the Sample IDs	seqVCF_SampID
Reformat VCF Files	seqBCF2GDS seqVCF2GDS