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 |
seqSetFilterCond | Set a Filter to Variant with Allele Count/Freq |
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 |