| Title: | Scientific Data Processing |
|---|---|
| Description: | This package provides a set of tools for processing scientific data. It's based on the exon Rust package. |
| Authors: | Trent Hauck [aut, cre] |
| Maintainer: | Trent Hauck <[email protected]> |
| License: | use_apache_license(version = 2, include_future = TRUE) |
| Version: | 0.9.0 |
| Built: | 2024-07-24 15:15:47 UTC |
| Source: | https://github.com/wheretrue/exon |
An ExonDataFrame is a data frame that is backed by an Exon engine.
new()
Initialize the ExonDataFrame object.
ExonDataFrame$new(result)
resultDataframe that serves as the base for ExonDataFrame.
to_arrow()
Convert the ExonDataFrame to an Arrow table.
ExonDataFrame$to_arrow()
An Arrow table.
to_record_batch_reader()
Convert the ExonDataFrame a stream of record batches.
ExonDataFrame$to_record_batch_reader()
A stream of record batches.
clone()
The objects of this class are cloneable with this method.
ExonDataFrame$clone(deep = FALSE)
deepWhether to make a deep clone.
An ExonRSessionContext is a context for an Exon session.
new()
Initialize the ExonRSessionContext object.
ExonRSessionContext$new()
sql()
Execute an SQL query.
ExonRSessionContext$sql(query)
queryThe SQL query to execute. Returns an ExonDataFrame.
execute()
Execute an SQL query.
ExonRSessionContext$execute(query)
queryThe SQL query to execute. Runs eagerly.
clone()
The objects of this class are cloneable with this method.
ExonRSessionContext$clone(deep = FALSE)
deepWhether to make a deep clone.
This function reads a BED file from a file and returns a RecordBatch stream.
read_bed_file(file_path)read_bed_file(file_path)
file_path |
The path to the BED file. |
A RecordBatch stream representing the contents of the BED table.
This function reads a FASTA file from a file and returns a RecordBatch stream.
read_fasta_file(file_path)read_fasta_file(file_path)
file_path |
The path to the FASTA file. |
A RecordBatch stream representing the contents of the FASTA table.
This function reads a FASTQ file from a file and returns a RecordBatch stream.
read_fastq_file(file_path)read_fastq_file(file_path)
file_path |
The path to the FASTQ file. |
A RecordBatch stream representing the contents of the FASTQ table.
This function reads a GenBank file from a file and returns a RecordBatch stream.
read_genbank_file(file_path)read_genbank_file(file_path)
file_path |
The path to the GenBank file. |
A RecordBatch stream representing the contents of the GenBank table.
This function reads a GFF file from a file and returns a RecordBatch stream.
read_gff_file(file_path)read_gff_file(file_path)
file_path |
The path to the GFF file. |
A RecordBatch stream representing the contents of the GFF table.
Copy the inferred exon table from the given path into the given stream.
read_inferred_exon_table(file_path, stream_ptr)read_inferred_exon_table(file_path, stream_ptr)
Copy the inferred exon table from the given path into the given stream.
read_inferred_exon_table_r(file_path, pointer_addr)read_inferred_exon_table_r(file_path, pointer_addr)
file_path |
The path to the inferred exon table. |
stream_ptr |
The pointer to the stream to copy the inferred exon table |
This function reads a MzML file from a file and returns a RecordBatch stream.
read_mzml_file(file_path)read_mzml_file(file_path)
file_path |
The path to the MzML file. |
A RecordBatch stream representing the contents of the MzML file.
This function reads a SAM file from a file and returns a RecordBatch stream. It will also read BAM files.
read_sam_file(file_path)read_sam_file(file_path)
file_path |
The path to the SAM/BAM file. |
A RecordBatch stream representing the contents of the SAM/BAM file.
This function reads a VCF/BCF file from a file and returns a RecordBatch stream.
read_vcf_file(file_path)read_vcf_file(file_path)
file_path |
The path to the VCF/BCF file. |
A RecordBatch stream representing the contents of the VCF/BCF file.