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 |