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


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Documentation for package ‘SeqArray’ version 1.42.2

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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