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")
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/SFFContainer-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: SFFContainer-class
> ### Title: Class '"SFFContainer"'
> ### Aliases: SFFContainer-class SFFContainer
> ### addRead,SFFContainer,SFFRead-method addRead
> ### getRead,SFFContainer,character-method getRead
> ### clipAdapterLeft<-,SFFContainer,numeric-method clipAdapterLeft<-
> ### clipAdapterLeft,SFFContainer-method clipAdapterLeft
> ### clipAdapterRight<-,SFFContainer,numeric-method clipAdapterRight<-
> ### clipAdapterRight,SFFContainer-method clipAdapterRight
> ### clipQualityLeft<-,SFFContainer,numeric-method clipQualityLeft<-
> ### clipQualityLeft,SFFContainer-method clipQualityLeft
> ### clipQualityRight<-,SFFContainer,numeric-method clipQualityRight<-
> ### clipQualityRight,SFFContainer-method clipQualityRight
> ### name<-,SFFContainer,character-method name<- name,SFFContainer-method
> ### name flowChars<-,SFFContainer,character-method flowChars<-
> ### flowChars,SFFContainer-method flowChars
> ### flowgramFormat<-,SFFContainer,numeric-method flowgramFormat<-
> ### flowgramFormat,SFFContainer-method flowgramFormat
> ### flowgrams<-,SFFContainer,list-method flowgrams<-
> ### flowgrams,SFFContainer-method flowgrams
> ### flowIndexes<-,SFFContainer,list-method flowIndexes<-
> ### flowIndexes,SFFContainer-method flowIndexes
> ### keySequence<-,SFFContainer,character-method keySequence<-
> ### keySequence,SFFContainer-method keySequence
> ### reads<-,SFFContainer,QualityScaledDNAStringSet-method reads<-
> ### reads,SFFContainer-method reads [,SFFContainer,ANY,ANY-method
> ### Keywords: classes
>
> ### ** Examples
>
> showClass("SFFContainer")
Class "SFFContainer" [package "R453Plus1Toolbox"]
Slots:
Name: name flowgramFormat
Class: character numeric
Name: flowChars keySequence
Class: character character
Name: clipQualityLeft clipQualityRight
Class: numeric numeric
Name: clipAdapterLeft clipAdapterRight
Class: numeric numeric
Name: flowgrams flowIndexes
Class: list list
Name: reads
Class: QualityScaledDNAStringSet
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.