DuckDB-Backed Interface for Large-Scale Genomic Data
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Documentation for package ‘dbSequence’ version 0.99.1
Help Pages
| asRanges | Extract genomic ranges from dbSequence objects |
| asRanges-method | Extract range columns as a view |
| as_granges | Convert objects to GRanges |
| as_granges.dbSequence | Convert objects to GRanges |
| as_granges.default | Convert objects to GRanges |
| as_ranges-dbSequence-method | Extract range columns as a view |
| coerce-method | Coercion methods between dbSequence and GRanges |
| coerce-methods | Coercion methods between dbSequence and GRanges |
| compute.dbSequence | Materialize a dbSequence in DuckDB |
| compute_coverage | Compute coverage over a region |
| compute_coverage.dbSequence | Compute coverage over a region |
| dbSequence | Constructor for dbSequence objects |
| dbSequence-class | dbSequence objects |
| DuckDBFile | Constructor for DuckDBFile objects |
| DuckDBFile-class | DuckDBFile objects |
| fileSource | Accessor for file_source slot |
| fileSource-method | Accessor for file_source slot |
| fileSource<- | Accessor for file_source slot |
| fileSource<--method | Accessor for file_source slot |
| filter_by_overlaps | Filter ranges by overlap |
| filter_by_overlaps.dbSequence | Filter ranges by overlap |
| import-method | Import BED files into DuckDB |
| import-method | Import BAM files into DuckDB |
| import-method | Import FASTA files into DuckDB |
| import-method | Import GFF files into DuckDB |
| import-method | Import GTF files into DuckDB |
| import-method | Import VCF files into DuckDB |
| import-method | Import character file paths into DuckDB (auto-detect format) |
| pool | Pool (aggregate) values by grouping columns |
| pool.dbSequence | Pool (aggregate) values by grouping columns |
| pool.default | Pool (aggregate) values by grouping columns |
| pool.tbl_dbi | Pool (aggregate) values by grouping columns |
| pool.tbl_duckdb_connection | Pool (aggregate) values by grouping columns |
| read_bam | Read a BAM file into DuckDB |
| read_bed | Read a BED file into DuckDB |
| read_gff | Read a GFF/GTF file into DuckDB |
| read_gff3 | Read a GFF/GTF file into DuckDB |
| read_vcf | Read a VCF file into DuckDB |
| show-method | Show method for DuckDBFile objects |
| show-method | Show method for dbSequence objects |
| tableName | Get table name from dbSequence |
| tableName-method | Get table name from dbSequence |