Big Data Management of Whole-genome Sequence Variant Calls


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Documentation for package ‘SeqArray’ version 1.12.9

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SeqArray-package Big Data Management of Whole-Genome Sequence Variant Calls
alt-method SeqVarGDSClass
asVCF-method SeqVarGDSClass
colData-method SeqVarGDSClass
filt-method SeqVarGDSClass
fixed-method SeqVarGDSClass
geno-method SeqVarGDSClass
granges-method SeqVarGDSClass
header-method SeqVarGDSClass
info-method SeqVarGDSClass
KG_P1_SampData Simulated sample data for 1000 Genomes Phase 1
qual-method SeqVarGDSClass
ref-method SeqVarGDSClass
rowRanges-method SeqVarGDSClass
seqAlleleCount Get Allele Frequencies or Counts
seqAlleleFreq Get Allele Frequencies or Counts
seqApply Apply Functions Over Array Margins
SeqArray 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
seqClose-method 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
seqGetParallel Setup/Get a Parallel Environment
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
seqParApply Apply Functions in Parallel
seqResetFilter Set a Filter to Sample or Variant
seqSetFilter Set a Filter to Sample or Variant
seqSetFilter-method Set a Filter to Sample or Variant
seqSetFilterChrom 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
SeqVarGDSClass SeqVarGDSClass
SeqVarGDSClass-class SeqVarGDSClass
seqVCF2GDS Reformat VCF Files
seqVCF_Header Parse the Header of a VCF File
seqVCF_SampID Get the Sample IDs