Package 'exonr'

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: 0.8.1
Built: 2024-04-19 05:21:25 UTC
Source: https://github.com/wheretrue/exon

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An ExonDataFrame is a data frame that is backed by an Exon engine.

Description

An ExonDataFrame is a data frame that is backed by an Exon engine.

Methods

Public methods


Method new()

Initialize the ExonDataFrame object.

Usage
ExonDataFrame$new(result)
Arguments
result

Dataframe that serves as the base for ExonDataFrame.


Method to_arrow()

Convert the ExonDataFrame to an Arrow table.

Usage
ExonDataFrame$to_arrow()
Returns

An Arrow table.


Method clone()

The objects of this class are cloneable with this method.

Usage
ExonDataFrame$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.


ExonR

Description

ExonR


An ExonRSessionContext is a context for an Exon session.

Description

An ExonRSessionContext is a context for an Exon session.

Methods

Public methods


Method new()

Initialize the ExonRSessionContext object.

Usage
ExonRSessionContext$new()

Method sql()

Execute an SQL query.

Usage
ExonRSessionContext$sql(query)
Arguments
query

The SQL query to execute. Returns an ExonDataFrame.


Method execute()

Execute an SQL query.

Usage
ExonRSessionContext$execute(query)
Arguments
query

The SQL query to execute. Runs eagerly.


Method clone()

The objects of this class are cloneable with this method.

Usage
ExonRSessionContext$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.


Read BED File

Description

This function reads a BED file from a file and returns a RecordBatch stream.

Usage

read_bed_file(file_path)

Arguments

file_path

The path to the BED file.

Value

A RecordBatch stream representing the contents of the BED table.


Read FASTA File

Description

This function reads a FASTA file from a file and returns a RecordBatch stream.

Usage

read_fasta_file(file_path)

Arguments

file_path

The path to the FASTA file.

Value

A RecordBatch stream representing the contents of the FASTA table.


Read FASTQ File

Description

This function reads a FASTQ file from a file and returns a RecordBatch stream.

Usage

read_fastq_file(file_path)

Arguments

file_path

The path to the FASTQ file.

Value

A RecordBatch stream representing the contents of the FASTQ table.


Read GenBank File

Description

This function reads a GenBank file from a file and returns a RecordBatch stream.

Usage

read_genbank_file(file_path)

Arguments

file_path

The path to the GenBank file.

Value

A RecordBatch stream representing the contents of the GenBank table.


Read GFF File

Description

This function reads a GFF file from a file and returns a RecordBatch stream.

Usage

read_gff_file(file_path)

Arguments

file_path

The path to the GFF file.

Value

A RecordBatch stream representing the contents of the GFF table.


Copy the inferred exon table from the given path into the given stream.

Description

Copy the inferred exon table from the given path into the given stream.

Usage

read_inferred_exon_table(file_path, stream_ptr)

Copy the inferred exon table from the given path into the given stream.

Description

Copy the inferred exon table from the given path into the given stream.

Usage

read_inferred_exon_table_r(file_path, pointer_addr)

Arguments

file_path

The path to the inferred exon table.

stream_ptr

The pointer to the stream to copy the inferred exon table


Read MzML File

Description

This function reads a MzML file from a file and returns a RecordBatch stream.

Usage

read_mzml_file(file_path)

Arguments

file_path

The path to the MzML file.

Value

A RecordBatch stream representing the contents of the MzML file.


Read SAM/BAM File

Description

This function reads a SAM file from a file and returns a RecordBatch stream. It will also read BAM files.

Usage

read_sam_file(file_path)

Arguments

file_path

The path to the SAM/BAM file.

Value

A RecordBatch stream representing the contents of the SAM/BAM file.


Read VCF/BCF File

Description

This function reads a VCF/BCF file from a file and returns a RecordBatch stream.

Usage

read_vcf_file(file_path)

Arguments

file_path

The path to the VCF/BCF file.

Value

A RecordBatch stream representing the contents of the VCF/BCF file.