R6 Class for loading and analysing nanopore (and other) FASTQ files

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

Super class

floundeR::FloundeR -> Fastq

Public fields

fastq_file

the file.path to the query FASTQ file

Active bindings

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.

Methods

Public methods

• Fastq$new()

• Fastq$as_tibble()

• Fastq$sequence_chunks()

• Fastq$get_sequence_chunk()

• Fastq$clone()

Inherited methods

• floundeR::FloundeR$bin_data()
• floundeR::FloundeR$num_scale()
• floundeR::FloundeR$nums_scale()
• floundeR::FloundeR$print()

---

Method new()

Creates a new Fastq 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

Fastq$new(fastq_file)

Arguments

fastq_file

The source sequencing_summary file.

Returns

A new Fastq object.

Examples

canonical_fastq <- flnDr("example.fastq.gz")
fastq <- Fastq$new(canonical_fastq)

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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

Fastq$as_tibble()

Returns

A tibble representation of the starting dataset

---

Method sequence_chunks()

Split the fastq sequence file explored by the package into sequence chunks for e.g. import into a relational database.

Usage

Fastq$sequence_chunks(chunk_size = 10000)

Arguments

chunk_size

The number of fastq entries that should be contained within a single chunk (default: 10000)

Returns

an invisible integer that defines the number of possible chunks; this can for example be iterated over

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Method get_sequence_chunk()

Get a chunk of fastq sequences from a larger monolithic file. This method can be called for up to $sequence_chunks() times or until NULL results are returned.

Usage

Fastq$get_sequence_chunk()

Returns

tibble containing the fastq entries corresponding to the available sequence chunk.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Fastq$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

## ------------------------------------------------
## Method `Fastq$new`
## ------------------------------------------------

canonical_fastq <- flnDr("example.fastq.gz")
fastq <- Fastq$new(canonical_fastq)
#> → opening fastq stream