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

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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