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R6 Class for loading and analysing nanopore sequencing_summary files

Source: R/sequencing_summary.R
SequencingSummary.Rd

This class aims to simplify the handling and exploration of sequencing_summary files and provides simple methods for accessing information that can be used to assess the performance of a run.

Super class

floundeR::FloundeR -> SequencingSummary

Public fields

sequencing_summary_file

the file.path to the query sequencing summary file

barcoding_summary_file

the file.path to the query barcoding summary file

Active bindings

flowcell

The sequencing summary file contains a collection of data that includes channel data. The channel data can be overlaid on spatial representations of flowcell layout to address spatial issues and to visualise the overall flowcell characteristics. This method creates a flowcell object that is suitable for these purposes.

sequencingset

The sequencingset active binding returns a sequencingset object that is canonically structured around the passes_filtering logical field to allow assessment of sequencing characteristics.

temporalset

The temporalset active binding prepares a temporalset object that is suitable for the temporal analysis of information within the sequencing summary file.

demultiplex

The demultiplex active binding prepared a multiplexset object that can be used to explore the barcoded content contained within the sequencing summary file and to access attributes that are related to these information.

Methods

Public methods

Inherited methods

Method new()

Creates a new SequencingSummary object. This initialisation method performs other sanity checking of the defined file(s) to ensure that it is indeed parseable and creates the required data structures.

Usage

SequencingSummary$new(sequencing_summary_file, barcoding_summary_file = NA)

Arguments

sequencing_summary_file

The source sequencing_summary file.

barcoding_summary_file

The source barcoding_summary_file file.

Returns

A new SequencingSummary object.

Examples

sequencing_summary <- flnDr("sequencing_summary.txt.bz2")
barcodes_summary <- flnDr("barcoding_summary.txt.bz2")
seqsum <- SequencingSummary$new(sequencing_summary, barcodes_summary)

Method as_tibble()

Export the imported dataset(s) as a tibble

This object consumes a sequencing summary file (and optionally the corresponding barcoding_summary file) and creates an object in memory that can be explored, sliced and filtered. This method dumps out the in-memory object for further exploration and development.

Usage

SequencingSummary$as_tibble()

Returns

A tibble representation of the starting dataset

Method clone()

The objects of this class are cloneable with this method.

Usage

SequencingSummary$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples


## ------------------------------------------------
## Method `SequencingSummary$new`
## ------------------------------------------------

sequencing_summary <- flnDr("sequencing_summary.txt.bz2")
barcodes_summary <- flnDr("barcoding_summary.txt.bz2")
seqsum <- SequencingSummary$new(sequencing_summary, barcodes_summary)