SFFContainer-class: Class '"SFFContainer"'

In R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System

Description

This class is a container for data from files in Roche's Standard Flowgram Format (SFF).

Objects from the Class

Objects can be created by calls of the form new("SFFContainer", ...). Usually, objects will be created by calling the readSFF method on a file in SFF format.

Slots

name:

Object of class "character" containing the name of the file this SFFContainer was created from.

flowgramFormat:

Object of class "numeric" representing the format used to encode each of the flowgram values for each read. Currently, only one flowgram format has been adopted and is coded by the value 1.

flowChars:

Object of class "character" containing the array of nucleotide bases ('A', 'C', 'G', 'T') that correspond to the nucleotides used for each flow of each read.

keySequence:

Object of class "character" representing the nucleotide bases of the key sequence used for these reads.

clipQualityLeft:

Object of class "numeric" representing the position of the first base after the clipping point for an attached quality sequence for each read. If only a combined (quality+adapter) clipping position is computed it should be stored in clipQualityLeft. If no clipping value is computed the field is set to 0. The position values use 1-based indexing.

clipQualityRight:

Object of class "numeric" representing the position of the last base before the clipping point for an attached quality sequence for each read. If only a combined (quality+adapter) clipping position is computed it should be stored in clipQualityRight. If no clipping value is computed the field is set to 0. The position values use 1-based indexing.

clipAdapterLeft:

Object of class "numeric" representing the position of the first base after the clipping point for an attached adapter sequence for each read. If only a combined (quality+adapter) clipping position is computed it should be stored in clipQualityLeft. If no clipping value is computed the field is set to 0. The position values use 1-based indexing.

clipAdapterRight:

Object of class "numeric" representing the position of the last base before the clipping point for an attached adapter sequence for each read. If only a combined (quality+adapter) clipping position is computed it should be stored in clipQualityRight. If no clipping value is computed the field is set to 0. The position values use 1-based indexing.

flowgrams:

Object of class "list" containing the homopolymer stretch estimates for each flow using one list item for each read.

flowIndexes:

Object of class "list" containing the flow positions for each base in the called sequence, i.e. for each base, the position in the flowgram whose estimate resulted in that base being called. Each read has its own list item.

reads:

Object of class "QualityScaledDNAStringSet" containing the basecalled nucleotide sequences of each read together with the quality scores for each of the bases in the sequence using the standard -log10 probability scale.

Methods

addRead

signature(object = "SFFContainer", read = "SFFRead"): Adds an object of class SFFRead to the SFFContainer

getRead

signature(object = "SFFContainer", readname = "character"): Returns the read with the given name as an object of class SFFRead.

clipAdapterLeft<-

signature(object = "SFFContainer", value = "numeric"): Setter-method for the clipAdapterLeft slot.

clipAdapterLeft

signature(object = "SFFContainer"): Getter-method for the clipAdapterLeft slot.

clipAdapterRight<-

signature(object = "SFFContainer", value = "numeric"): Setter-method for the clipAdapterRight slot.

clipAdapterRight

signature(object = "SFFContainer"): Getter-method for the clipAdapterRight slot.

clipQualityLeft<-

signature(object = "SFFContainer", value = "numeric"): Setter-method for the clipQualityLeft slot.

clipQualityLeft

signature(object = "SFFContainer"): Getter-method for the clipQualityLeft slot.

clipQualityRight<-

signature(object = "SFFContainer", value = "numeric"): Setter-method for the clipQualityRight slot.

clipQualityRight

signature(object = "SFFContainer"): Getter-method for the clipQualityRight slot.

name<-

signature(object = "SFFContainer", value = "character"): Setter-method for the name slot.

name

signature(object = "SFFContainer"): Getter-method for the name slot.

flowChars<-

signature(object = "SFFContainer", value = "character"): Setter-method for the flowChars slot.

flowChars

signature(object = "SFFContainer"): Getter-method for the flowChars slot.

flowgramFormat<-

signature(object = "SFFContainer", value = "numeric"): Setter-method for the flowgramFormat slot.

flowgramFormat

signature(object = "SFFContainer"): Getter-method for the flowgramFormat slot.

flowgrams<-

signature(object = "SFFContainer", value = "list"): Setter-method for the flowgrams slot.

flowgrams

signature(object = "SFFContainer"): Getter-method for the flowgrams slot.

flowIndexes<-

signature(object = "SFFContainer", value = "list"): Setter-method for the flowIndexes slot.

flowIndexes

signature(object = "SFFContainer"): Getter-method for the flowIndexes slot.

keySequence<-

signature(object = "SFFContainer", value = "character"): Setter-method for the keySequence slot.

keySequence

signature(object = "SFFContainer"): Getter-method for the keySequence slot.

reads<-

signature(object = "SFFContainer", value = "QualityScaledDNAStringSet"): Setter-method for the reads slot.

reads

signature(object = "SFFContainer"): Getter-method for the reads slot.

[

signature(x = "SFFContainer", i = "ANY", j = "ANY"): Subsetting a SFFContainer object.

Author(s)

Christian Ruckert

See Also

readSFF, SFFRead

Examples

  showClass("SFFContainer")

R453Plus1Toolbox documentation built on Nov. 8, 2020, 5:59 p.m.