Man pages for zhengxwen/SeqArray
Data Management of Large-Scale Whole-Genome Sequence Variant Calls
| KG_P1_SampData | Simulated sample data for 1000 Genomes Phase 1 |
| seqAddValue | Add values to a GDS File |
| seqAlleleFreq | Get Allele Frequencies or Counts |
| seqApply | Apply Functions Over Array Margins |
| SeqArray-package | Data Management of Large-scale Whole-Genome Sequence Variant... |
| seqAsVCF | VariantAnnotation objects |
| 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 |
| seqDelete | Delete GDS Variables |
| seqDigest | Hash function digests |
| seqEmptyFile | Empty GDS file |
| seqExampleFileName | Example files |
| seqExport | Export to a GDS File |
| seqGDS2SNP | Convert to a SNP GDS File |
| seqGDS2VCF | Convert to a VCF File |
| seqGet2bGeno | Get packed genotypes |
| seqGetData | Get Data |
| seqGetFilter | Get the Filter of GDS File |
| seqMerge | Merge Multiple SeqArray GDS Files |
| seqMissing | Missing genotype percentage |
| 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 |
| seqRecompress | Recompress the GDS file |
| seqResetVariantID | Reset Variant ID in SeqArray GDS Files |
| seqSetFilter | 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 |
| seqUnitApply | Apply Function Over Variant Units |
| seqUnitFilterCond | Filter unit variants |
| seqUnitSlidingWindows | Sliding units of selected variants |
| seqUnitSubset | Subset and merge the units |
| SeqVarGDSClass-class | SeqVarGDSClass |
| seqVCF2GDS | Reformat VCF Files |
| seqVCF_Header | Parse the Header of a VCF/BCF File |
| seqVCF_SampID | Get the Sample IDs |
