# Data Management of Large-Scale Whole-Genome Sequence Variant Calls

## Documentation for package ‘SeqArray’ version 1.42.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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