SequencingSummary.RdThis 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.
floundeR::FloundeR -> SequencingSummary
sequencing_summary_filethe file.path to the query FAST5 file
barcoding_summary_filethe file.path to the query FAST5 file
flowcellThe 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.
sequencingsetThe sequencingset active binding returns a sequencingset object
that is canonically structured around the passes_filtering logical
field to allow assessment of sequencing characteristics.
temporalsetThe temporalset active binding prepares a temporalset object that
is suitable for the temporal analysis of information within the
sequencing summary file.
demultiplexThe 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.
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.
SequencingSummary$new(sequencing_summary_file, barcoding_summary_file = NA)
sequencing_summary_fileThe source sequencing_summary file.
barcoding_summary_fileThe source barcoding_summary_file file.
A new Fast5 object.
sequencing_summary <- flnDr("sequencing_summary.txt.bz2") barcodes_summary <- flnDr("barcoding_summary.txt.bz2") seqsum <- SequencingSummary$new(sequencing_summary, barcodes_summary)
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.
SequencingSummary$as_tibble()
A tibble representation of the starting dataset
clone()The objects of this class are cloneable with this method.
SequencingSummary$clone(deep = FALSE)
deepWhether to make a deep clone.
## ------------------------------------------------ ## Method `SequencingSummary$new` ## ------------------------------------------------ sequencing_summary <- flnDr("sequencing_summary.txt.bz2") barcodes_summary <- flnDr("barcoding_summary.txt.bz2") seqsum <- SequencingSummary$new(sequencing_summary, barcodes_summary)