Class "SFFRead"

Description

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

Objects from the Class

Objects can be created by calls of the form new("SFFRead", ...). Usually, objects will be created by calling the getRead method on an object of class SFFContainer.

Slots

name:

Object of class "character" representing the name of the read.

read:

Object of class "DNAString" containing the basecalled nucleotide sequence of the read.

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. 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. 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. 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. 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.

flowgram:

Object of class "numeric" containing the homopolymer stretch estimates for each flow.

flowIndexes:

Object of class "numeric" 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.

quality:

Object of class "BString" containing the quality scores for each of the bases in the sequence, where the values use the standard -log10 probability scale.

Methods

read<-

signature(object = "SFFRead", value = "DNAString"): Setter-method for the read slot.

read

signature(object = "SFFRead"): Getter-method for the read 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.

keySequence<-

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

keySequence

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

clipAdapterLeft<-

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

clipAdapterLeft

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

clipAdapterRight<-

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

clipAdapterRight

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

clipQualityLeft<-

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

clipQualityLeft

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

clipQualityRight<-

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

clipQualityRight

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

flowgram<-

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

flowgram

signature(object = "SFFRead"): Getter-method for the flowgram slot.

flowIndexes<-

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

flowIndexes

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

name<-

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

name

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

quality<-

signature(object = "SFFRead", value = "BString"): Setter-method for the quality slot.

quality

signature(object = "SFFRead"): Getter-method for the quality slot.

Author(s)

Christian Ruckert

See Also

readSFF, SFFContainer

Examples

showClass("SFFRead")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(R453Plus1Toolbox)
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/R453Plus1Toolbox/SFFRead-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: SFFRead-class
> ### Title: Class '"SFFRead"'
> ### Aliases: SFFRead-class SFFRead
> ###   read<-,SFFRead,QualityScaledDNAStringSet-method read<-
> ###   read,SFFRead-method read flowChars<-,SFFRead,character-method
> ###   flowChars,SFFRead-method flowgramFormat<-,SFFRead,numeric-method
> ###   flowgramFormat,SFFRead-method keySequence<-,SFFRead,character-method
> ###   keySequence,SFFRead-method clipAdapterLeft<-,SFFRead,numeric-method
> ###   clipAdapterLeft,SFFRead-method
> ###   clipAdapterRight<-,SFFRead,numeric-method
> ###   clipAdapterRight,SFFRead-method
> ###   clipQualityLeft<-,SFFRead,numeric-method
> ###   clipQualityLeft,SFFRead-method
> ###   clipQualityRight<-,SFFRead,numeric-method
> ###   clipQualityRight,SFFRead-method flowgram<-,SFFRead,numeric-method
> ###   flowgram<- flowgram,SFFRead-method flowgram
> ###   flowIndexes<-,SFFRead,numeric-method flowIndexes,SFFRead-method
> ###   name<-,SFFRead,character-method name,SFFRead-method quality<-
> ###   quality<-,SFFRead,BString-method quality,SFFRead-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("SFFRead")
Class "SFFRead" [package "R453Plus1Toolbox"]

Slots:
                                                                          
Name:              name   flowgramFormat        flowChars      keySequence
Class:        character          numeric        character        character
                                                                          
Name:   clipQualityLeft clipQualityRight  clipAdapterLeft clipAdapterRight
Class:          numeric          numeric          numeric          numeric
                                                                          
Name:          flowgram      flowIndexes             read          quality
Class:          numeric          numeric        DNAString          BString
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>