IONiseR (version 1.2.2)

readInfo,Fast5Summary-method: An S4 class for summarised data from a MinION sequencing run

Description

An S4 class for summarised data from a MinION sequencing run

Usage

"readInfo"(x)
"rawData"(x)
"baseCalled"(x)
"fastq"(x)
"["(x, i)
"fastqTemplate"(x)
"fastqComplement"(x)
"fastq2D"(x)
"length"(x)

Arguments

x

Object of class Fast5Summary

i

Vector defining index to subset by.

Value

An object of class Fast5Summary

Methods (by generic)

• readInfo: Returns readInfo data.table
• rawData: Returns rawData data.table
• baseCalled: Returns baseCalled data.table
• fastq: Returns ShortReadQ object stored in fastq slot.
• [: Subset object and return an object of the same class.
• fastqTemplate: Returns ShortReadQ object containing only template reads
• fastqComplement: Returns ShortReadQ object containing only complement reads
• fastq2D: Returns ShortReadQ object containing only 2D reads
• length: Returns the number of files read during creation of the object

Slots

readInfo

Object of class data.table. Contains five columns:

• id - an integer key that allows use to match entries in the separate slots of this object.
• file - Basename of the fast5 file the data was read from.
• read - Read number from channel.
• channel - channel.
• mux - Specific pore that was used within the four that are assigned to a single channel. Should be in the range 1-4, but if this isn't available it will be 0.

rawData

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

• id - an integer key that allows use to match entries in the separate slots of this object.
• start_time - time in seconds after the run started that this reading began.
• duration - time in seconds the reading lasted.
• num_events - the number of events that were recorded as part of this reading.
• median_signal - median of the recorded signals for this set of events.

baseCalled

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

• id - an integer key that allows use to match entries in the separate slots of this object.
• start_time - time in seconds after the run started that this reading began.
• duration - time in seconds the reading lasted.
• num_events - the number of events that were recorded as part of this reading.
• strand - can be either 'template' or 'complement'
• full_2D - boolean value specifying whether the read forms part of a 2D pair. If TRUE the FASTQ data for the template, complement and 2D read will be available in the @fastq slot.

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.

Examples

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