This class is a container for information on a specific 4C-seq experiment. Stored information includes raw reads, fragment data, and the experiment's viewpoint location.
Objects from the Class
Objects can be created by calls of the form new("Data4Cseq", ...).
Slots
viewpointChromosome:
Object of class "character" representing the viewpoint chromosome's name
viewpointInterval:
Object of class "numeric" representing the viewpoint interval's location
readLength:
Object of class "numeric" representing the experiment's read length
pointsOfInterest:
Object of class "data.frame" representing any points of interest to be marked in the near-cis visualizations
rawReads:
Object of class "GAlignments" representing the raw 4C-seq reads of the experiment
rawFragments:
Object of class "data.frame" representing the experiment's corresponding virtual fragment library
nearCisFragments:
Object of class "data.frame" representing near-cis data in fragment form
Methods
viewpointChromosome<-
signature(object = "Data4Cseq", value = "character"):
Setter-method for the viewpointChromosome slot.
viewpointChromosome
signature(object = "Data4Cseq"):
Getter-method for the viewpointChromosome slot.
viewpointInterval<-
signature(object = "Data4Cseq", value = "numeric"):
Setter-method for the viewpointInterval slot.
viewpointInterval
signature(object = "Data4Cseq"):
Getter-method for the viewpointInterval slot.
readLength<-
signature(object = "Data4Cseq", value = "numeric"):
Setter-method for the readLength slot.
readLength
signature(object = "Data4Cseq"):
Getter-method for the readLength slot.
pointsOfInterest<-
signature(object = "Data4Cseq", value = "data.frame"):
Setter-method for the pointsOfInterest slot.
pointsOfInterest
signature(object = "Data4Cseq"):
Getter-method for the pointsOfInterest slot.
rawReads<-
signature(object = "Data4Cseq", value = "GAlignments"):
Setter-method for the rawReads slot.
rawReads
signature(object = "Data4Cseq"):
Getter-method for the rawReads slot.
rawFragments<-
signature(object = "Data4Cseq", value = "data.frame"):
Setter-method for the rawFragments slot.
rawFragments
signature(object = "Data4Cseq"):
Getter-method for the rawFragments slot.
nearCisFragments<-
signature(object = "Data4Cseq", value = "data.frame"):
Setter-method for the nearCisFragments slot.
nearCisFragments
signature(object = "Data4Cseq"):
Getter-method for the nearCisFragments slot.
Author(s)
Carolin Walter
Examples
showClass("Data4Cseq")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(Basic4Cseq)
Loading required package: Biostrings
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: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomicAlignments
Loading required package: GenomeInfoDb
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: caTools
Attaching package: 'caTools'
The following object is masked from 'package:IRanges':
runmean
The following object is masked from 'package:S4Vectors':
runmean
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Basic4Cseq/Data4Cseq-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Data4Cseq-class
> ### Title: Class '"Data4Cseq"'
> ### Aliases: Data4Cseq-class viewpointChromosome
> ### viewpointChromosome,Data4Cseq-method viewpointChromosome<-
> ### viewpointChromosome<-,Data4Cseq,character-method viewpointInterval
> ### viewpointInterval,Data4Cseq-method viewpointInterval<-
> ### viewpointInterval<-,Data4Cseq,numeric-method readLength
> ### readLength,Data4Cseq-method readLength<-
> ### readLength<-,Data4Cseq,numeric-method pointsOfInterest
> ### pointsOfInterest,Data4Cseq-method pointsOfInterest<-
> ### pointsOfInterest<-,Data4Cseq,data.frame-method rawReads
> ### rawReads,Data4Cseq-method rawReads<-
> ### rawReads<-,Data4Cseq,GAlignments-method rawFragments
> ### rawFragments,Data4Cseq-method rawFragments<-
> ### rawFragments<-,Data4Cseq,data.frame-method nearCisFragments
> ### nearCisFragments,Data4Cseq-method nearCisFragments<-
> ### nearCisFragments<-,Data4Cseq,data.frame-method
> ### Keywords: classes
>
> ### ** Examples
>
> showClass("Data4Cseq")
Class "Data4Cseq" [package "Basic4Cseq"]
Slots:
Name: viewpointChromosome viewpointInterval readLength
Class: character numeric numeric
Name: pointsOfInterest rawReads rawFragments
Class: data.frame GAlignments data.frame
Name: nearCisFragments
Class: data.frame
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.