Fastq.RdThis 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.
floundeR::FloundeR -> Fastq
fastq_filethe file.path to the query FASTQ file
sequencingsetThe sequencingset active binding returns a sequencingset object
that is canonically structured around the passes_filtering logical
field to allow assessment of sequencing characteristics.
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.
Fastq$new(fastq_file)
fastq_fileThe source sequencing_summary file.
A new Fastq object.
canonical_fastq <- flnDr("example.fastq.gz") fastq <- Fastq$new(canonical_fastq)
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.
Fastq$as_tibble()
A tibble representation of the starting dataset
sequence_chunks()Split the fastq sequence file explored by the package into sequence chunks for e.g. import into a relational database.
Fastq$sequence_chunks(chunk_size = 10000)
chunk_sizeThe number of fastq entries that should be contained within a single chunk (default: 10000)
an invisible integer that defines the number of possible chunks; this can for example be iterated over
get_sequence_chunk()Get a chunk of fastq sequences from a larger monolithic file. This method
can be called for up to $sequence_chunks() times or until NULL results
are returned.
Fastq$get_sequence_chunk()
tibble containing the fastq entries corresponding to the available sequence chunk.
clone()The objects of this class are cloneable with this method.
Fastq$clone(deep = FALSE)
deepWhether to make a deep clone.
## ------------------------------------------------ ## Method `Fastq$new` ## ------------------------------------------------ canonical_fastq <- flnDr("example.fastq.gz") fastq <- Fastq$new(canonical_fastq) #> → opening fastq stream