Fastq: R6 Class for loading and analysing nanopore (and other) FASTQ...
In sagrudd/floundeR: Toolkit For Nanopore Sequence Analysis
Fastq R Documentation
R6 Class for loading and analysing nanopore (and other) FASTQ files
Description
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_filethe file.path
to the query FASTQ file
Active bindings
sequencingsetThe 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
Inherited methods
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$new(fastq_file)
Arguments
fastq_fileThe source
sequencing_summary file.
Returns
A new Fastq object.
Examples
canonical_fastq <- flnDr("example.fastq.gz")
fastq <- Fastq$new(canonical_fastq)
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_sizeThe 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
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$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Examples
## ------------------------------------------------
## Method `Fastq$new`
## ------------------------------------------------
canonical_fastq <- flnDr("example.fastq.gz")
fastq <- Fastq$new(canonical_fastq)
sagrudd/floundeR documentation built on Nov. 18, 2022, 10:31 a.m.
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| Fastq | R Documentation |
R6 Class for loading and analysing nanopore (and other) FASTQ files
Description
This class aims to simplify the handling and exploration of FASTQ files and provides simple methods for accessing information that can be used to assess the contents of a FASTQ file.
Super class
floundeR::FloundeR -> Fastq
Public fields
fastq_filethe file.path to the query FASTQ file
Active bindings
sequencingsetThe
sequencingsetactive binding returns a sequencingset object that is canonically structured around thepasses_filteringlogical field to allow assessment of sequencing characteristics.
Methods
Public methods
Inherited methods
Method new()
Creates a new Fastq object. This initialisation method performs other sanity checking of the defined file(s) to ensure that it is indeed parseable and creates the required data structures.
Usage
Fastq$new(fastq_file)
Arguments
fastq_fileThe source sequencing_summary file.
Returns
A new Fastq object.
Examples
canonical_fastq <- flnDr("example.fastq.gz")
fastq <- Fastq$new(canonical_fastq)
Method as_tibble()
Export the imported dataset(s) as a tibble
This object consumes a sequencing summary file (and optionally the corresponding barcoding_summary file) and creates an object in memory that can be explored, sliced and filtered. This method dumps out the in-memory object for further exploration and development.
Usage
Fastq$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_sizeThe 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
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$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Examples
## ------------------------------------------------
## Method `Fastq$new`
## ------------------------------------------------
canonical_fastq <- flnDr("example.fastq.gz")
fastq <- Fastq$new(canonical_fastq)
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