Fast5: R6 Class for loading and analysing nanopore FAST5 sequence...
In sagrudd/floundeR: Toolkit For Nanopore Sequence Analysis
Fast5 R Documentation
R6 Class for loading and analysing nanopore FAST5 sequence files
Description
This class aims to simplify the handling and exploration of FAST5 files and
provides simple methods for accessing information that can be used to
identify the sequencing platform, flowcell used, sequencing kit and other
metainformation that includes whether they are single- or- multi format
files.
Public fields
fast5_filethe file.path to the query FAST5 file
Methods
Public methods
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Method new()
Creates a new Fast5 object. This initialisation method performs other
sanity checking of the defined file to ensure that it is indeed a
file, a single file, is in HDF5 format and is either single- or
multi-FAST5 compliant
Usage
Fast5$new(fast5_file = NA)
Arguments
fast5_fileThe source FAST5 file.
Returns
A new Fast5 object.
Method is_single_fast5()
Check if a provided file corresponds to a single entry FAST5 file
Simple method to check whether the provided file path corresponds to
a valid FAST5 file and if this file corresponds to a single FAST5
format.
Usage
Fast5$is_single_fast5()
Returns
boolean
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$is_single_fast5()
Method is_multi_fast5()
Check if a provided file corresponds to a multiple entry FAST5 file
Simple method to check whether the provided file path corresponds to
a valid FAST5 file and if this file corresponds to a multi FAST5
format.
Usage
Fast5$is_multi_fast5()
Returns
boolean
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$is_multi_fast5()
Method get_platform()
Extract the sequencing platform identified within a FAST5 file
This method parses a FAST5 sequence file and extracts the information
on specified sequencing platform - this can be used to identify e.g.
gridion or promethion based information.
Usage
Fast5$get_platform()
Returns
vector of platform
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_platform()
Method get_flowcell_id()
Extract the flowcell_id identified within a FAST5 file
This method parses a FAST5 sequence file and extracts the information
on specified flowcell_id - this can be used to track flowcells used
within a laboratory
Usage
Fast5$get_flowcell_id()
Returns
vector of flowcell_id
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_flowcell_id()
Method get_exp_start_time()
Extract the experiment start time identified within a FAST5 file
This method parses a FAST5 sequence file and extracts the information
on specified experiment start time - this can be used in
palaeogenomics of such ancient datasets. Please note that the sampled
start time is transformed using lubridate for presentation.
Usage
Fast5$get_exp_start_time()
Returns
vector of experiment_start_time
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_exp_start_time()
Method get_read_count()
Extract the number of reads identified within a FAST5 file
This method parses a FAST5 sequence file and extracts the information
on the read count - this is a simple count only
Usage
Fast5$get_read_count()
Returns
integer count of reads
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_read_count()
Method get_flowcell_type()
Extract the flowcell type identified within a FAST5 file
This method parses a FAST5 sequence file and extracts the information
on the flowcell type - this is based on user entry at start of run.
Usage
Fast5$get_flowcell_type()
Returns
vector of flowcell_types
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_flowcell_type()
Method get_sequencing_kit()
Extract the sequencing kit identified within a FAST5 file
This method parses a FAST5 sequence file and extracts the information
on the sequencing_kit used - this is based on user entry at start of
run.
Usage
Fast5$get_sequencing_kit()
Returns
vector of sequencing_kit
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_sequencing_kit()
Method get_info()
Extract salient experimental information from a FAST5 file
The FAST5 sequence file contains information relating to the
sequencing platform, flowcell and library preparation kits used in a
study. This method pulls these information into a data.frame.
Usage
Fast5$get_info(atomic = TRUE)
Arguments
atomicwhether a single entity (multi files only) should be
considered (FALSE)
Returns
data.frame
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_info(atomic=FALSE)
Method print()
print method to override the standard R6 printing
Usage
Fast5$print(...)
Arguments
...stuff passed onwards
Method clone()
The objects of this class are cloneable with this method.
Usage
Fast5$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Examples
## ------------------------------------------------
## Method `Fast5$is_single_fast5`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$is_single_fast5()
## ------------------------------------------------
## Method `Fast5$is_multi_fast5`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$is_multi_fast5()
## ------------------------------------------------
## Method `Fast5$get_platform`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_platform()
## ------------------------------------------------
## Method `Fast5$get_flowcell_id`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_flowcell_id()
## ------------------------------------------------
## Method `Fast5$get_exp_start_time`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_exp_start_time()
## ------------------------------------------------
## Method `Fast5$get_read_count`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_read_count()
## ------------------------------------------------
## Method `Fast5$get_flowcell_type`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_flowcell_type()
## ------------------------------------------------
## Method `Fast5$get_sequencing_kit`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_sequencing_kit()
## ------------------------------------------------
## Method `Fast5$get_info`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_info(atomic=FALSE)
sagrudd/floundeR documentation built on Nov. 18, 2022, 10:31 a.m.
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| Fast5 | R Documentation |
R6 Class for loading and analysing nanopore FAST5 sequence files
Description
This class aims to simplify the handling and exploration of FAST5 files and provides simple methods for accessing information that can be used to identify the sequencing platform, flowcell used, sequencing kit and other metainformation that includes whether they are single- or- multi format files.
Public fields
fast5_filethe file.path to the query FAST5 file
Methods
Public methods
Method new()
Creates a new Fast5 object. This initialisation method performs other sanity checking of the defined file to ensure that it is indeed a file, a single file, is in HDF5 format and is either single- or multi-FAST5 compliant
Usage
Fast5$new(fast5_file = NA)
Arguments
fast5_fileThe source FAST5 file.
Returns
A new Fast5 object.
Method is_single_fast5()
Check if a provided file corresponds to a single entry FAST5 file
Simple method to check whether the provided file path corresponds to a valid FAST5 file and if this file corresponds to a single FAST5 format.
Usage
Fast5$is_single_fast5()
Returns
boolean
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$is_single_fast5()
Method is_multi_fast5()
Check if a provided file corresponds to a multiple entry FAST5 file
Simple method to check whether the provided file path corresponds to a valid FAST5 file and if this file corresponds to a multi FAST5 format.
Usage
Fast5$is_multi_fast5()
Returns
boolean
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$is_multi_fast5()
Method get_platform()
Extract the sequencing platform identified within a FAST5 file
This method parses a FAST5 sequence file and extracts the information on specified sequencing platform - this can be used to identify e.g. gridion or promethion based information.
Usage
Fast5$get_platform()
Returns
vector of platform
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_platform()
Method get_flowcell_id()
Extract the flowcell_id identified within a FAST5 file
This method parses a FAST5 sequence file and extracts the information on specified flowcell_id - this can be used to track flowcells used within a laboratory
Usage
Fast5$get_flowcell_id()
Returns
vector of flowcell_id
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_flowcell_id()
Method get_exp_start_time()
Extract the experiment start time identified within a FAST5 file
This method parses a FAST5 sequence file and extracts the information
on specified experiment start time - this can be used in
palaeogenomics of such ancient datasets. Please note that the sampled
start time is transformed using lubridate for presentation.
Usage
Fast5$get_exp_start_time()
Returns
vector of experiment_start_time
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_exp_start_time()
Method get_read_count()
Extract the number of reads identified within a FAST5 file
This method parses a FAST5 sequence file and extracts the information on the read count - this is a simple count only
Usage
Fast5$get_read_count()
Returns
integer count of reads
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_read_count()
Method get_flowcell_type()
Extract the flowcell type identified within a FAST5 file
This method parses a FAST5 sequence file and extracts the information on the flowcell type - this is based on user entry at start of run.
Usage
Fast5$get_flowcell_type()
Returns
vector of flowcell_types
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_flowcell_type()
Method get_sequencing_kit()
Extract the sequencing kit identified within a FAST5 file
This method parses a FAST5 sequence file and extracts the information on the sequencing_kit used - this is based on user entry at start of run.
Usage
Fast5$get_sequencing_kit()
Returns
vector of sequencing_kit
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_sequencing_kit()
Method get_info()
Extract salient experimental information from a FAST5 file
The FAST5 sequence file contains information relating to the sequencing platform, flowcell and library preparation kits used in a study. This method pulls these information into a data.frame.
Usage
Fast5$get_info(atomic = TRUE)
Arguments
atomicwhether a single entity (multi files only) should be considered (FALSE)
Returns
data.frame
Examples
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_info(atomic=FALSE)
Method print()
print method to override the standard R6 printing
Usage
Fast5$print(...)
Arguments
...stuff passed onwards
Method clone()
The objects of this class are cloneable with this method.
Usage
Fast5$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Examples
## ------------------------------------------------
## Method `Fast5$is_single_fast5`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$is_single_fast5()
## ------------------------------------------------
## Method `Fast5$is_multi_fast5`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$is_multi_fast5()
## ------------------------------------------------
## Method `Fast5$get_platform`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_platform()
## ------------------------------------------------
## Method `Fast5$get_flowcell_id`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_flowcell_id()
## ------------------------------------------------
## Method `Fast5$get_exp_start_time`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_exp_start_time()
## ------------------------------------------------
## Method `Fast5$get_read_count`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_read_count()
## ------------------------------------------------
## Method `Fast5$get_flowcell_type`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_flowcell_type()
## ------------------------------------------------
## Method `Fast5$get_sequencing_kit`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_sequencing_kit()
## ------------------------------------------------
## Method `Fast5$get_info`
## ------------------------------------------------
promFast5 <- system.file("extdata", "prom.fast5", package="floundeR")
promF5 <- Fast5$new(fast5_file=promFast5)
promF5$get_info(atomic=FALSE)
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