Fast5Summary-class {IONiseR}R Documentation

An S4 class for summarised data from a MinION sequencing run

Description

An S4 class for summarised data from a MinION sequencing run

Usage

## S4 method for signature 'Fast5Summary'
length(x)

## S4 method for signature 'Fast5Summary'
readInfo(x)

## S4 method for signature 'Fast5Summary'
eventData(x)

## S4 method for signature 'Fast5Summary'
baseCalled(x)

## S4 method for signature 'Fast5Summary'
fastq(x)

## S4 method for signature 'Fast5Summary,ANY,ANY,ANY'
x[i]

## S4 method for signature 'Fast5Summary'
fastqTemplate(x)

## S4 method for signature 'Fast5Summary'
fastqComplement(x)

## S4 method for signature 'Fast5Summary'
fastq2D(x)

Arguments

x

Object of class Fast5Summary

i

Vector defining index to subset by.

Value

An object of class Fast5Summary

Methods (by generic)

Slots

readInfo

Object of class tibble. Contains five columns:

rawData

Object of class tibble. Intended to hold raw signal data although reading this is currently not implemented in IONiseR.

eventData

Object of class tibble. Holds summary of events data prior to base calling. Contains five columns:

baseCalled

Object of class tibble. For the most part contains similar data to the @eventData slot, the base called data is derived from it.

fastq

Object of class ShortReadQ. This slot contains all reads (template, complement and 2D). The read names take the form NUM_STRAND, where NUM matches with the id column in the other slots and STRAND indicates whether the read is template, complement or 2D.

versions

A list intended to store the version of IONiseR that was used to create the object. (May be extended in the future to include the version of MinKNOW that the original fast5 files were processed, if this can be determined accurately.)

Examples

if( require(minionSummaryData) ) {
   data(s.typhi.rep2, package = 'minionSummaryData')
   length( s.typhi.rep2 )
}

[Package IONiseR version 2.16.0 Index]