A JunctionSeqCountSet is a container class that
contains all information pertaining to a JunctionSeq analysis
and dataset. In general, these methods and slots will not be used
by the end-users. In general, JunctionSeqCountSet objects will be
created by readJunctionSeqCounts or
runJunctionSeqAnalyses and are to be
manipulated byhigh-level JunctionSeq functions such as
estimateEffectSizes or fitJunctionSeqDispersionFunction.
The methods documented here are for use by advanced users only.
Details
Slots:
designColumns
A character vector with the column names in the design data.frame.
dispFitCoefs
The dispersion fit coefficients.
fittedMu
Fitted mu values generated by DESeq2 code.
dispFunctionType
A list of various variables defining the dispersion functon used.
dispFunction
A function that converts a base mean to a fitted dispersion based on all included count bins.
dispFunctionJct
A function that converts a base mean to a fitted dispersion based only on the splice junction bins.
dispFunctionExon
A function that converts a base mean to a fitted dispersion based only on the exon bins.
formulas
A list of formulas used.
annotationFile
The annotation file.
geneCountData
A matrix of the gene-level counts
countVectors
A matrix of the count vectors.
altSizeFactors
(Not currently used)
plottingEstimates
A list of fitted estimates, for plotting.
plottingEstimatesVST
(Not currently used)
geneLevelPlottingEstimates
A list of gene-level fitted estimates, for plotting.
modelFitForHypothesisTest
(Not currently used)
modelFitForEffectSize
(Not currently used)
flatGffData
A data.frame representation of the flattened gff annotation for each countbin.
flatGffGeneData
A data.frame representation of the flattened gff annotation for each gene.
analysisType
The type of analysis. Character string.
DESeqDataSet
The specially-constructed DESeqDataSet, to be passed to the internally-loaded DESeq2 code.
modelCoefficientsSample:
Object of class "list". Placeholder slot for model coefficients (used for diagnostic testing of code).
modelCoefficientsGene:
Object of class "list". Placeholder slot for model coefficients (used for diagnostic testing of code).
assayData:
Object of class "AssayData". Contains various data.
phenoData:
Object of class "AnnotatedDataFrame". Phenotype data.
featureData:
Object of class "AnnotatedDataFrame". Counting bin data.
experimentData:
Object of class "MIAxE". Information on the experiment.
annotation:
Object of class "character". Not used.
protocolData:
Object of class "AnnotatedDataFrame". Information on the code.
.__classVersion__:
Object of class "Versions". The version of the JunctionSeqCountSet.
Constructor
newJunctionSeqCountSet( countData,
geneCountData,
design,
geneIDs,
countbinIDs,
featureIntervals=NULL,
transcripts=NULL):
Creates a new JunctionSeqCountSet
countData
A matrix of junction-level count data of non-negative integer values.
The rows correspond to counts for each splice-junction counting bin,
the columns correspond to samples. Note that biological
replicates should each get their own column, while the
counts of technical replicates (i.e., several sequencing
runs/lanes from the same sample) should be summed up
into a single column.
geneCountData
A matrix of gene-level count data of non-negative integer values.
The rows correspond to counts for each gene,
the columns correspond to samples. Note that biological
replicates should each get their own column, while the
counts of technical replicates (i.e., several sequencing
runs/lanes from the same sample) should be summed up
into a single column. Must have the same dimensions as countData.
design
A data frame consisting of all factors to be included in the analysis.
All columns should be factors. Each column should represent a different variable,
each row should represent a different sample. The number of rows must equal the
number of columns in geneCountData and countData.
geneIDs
A character vector of gene indentifiers for each splice junction. The length must
equal the number of rows in countData.
countbinIDs
A character vector of splice-junction-locus indentifiers for each splice junction. The length must
equal the number of rows in countData.
featureIntervals
Optional. A data.frame with 4 columns: "chr", "start", "end", and "strand". chr and strand should
be character vectors or factors, start and end must be integers.
transcripts
Optional. Character vector listing the transcripts that each splice junction belongs to. Some junctions
may belong to more than one transcripts. In this case, transcripts should be separated with the "+" character.
This constructor function SHOULD NOT BE USED in normal operation.
Instead you should use the readJunctionSeqCounts
function, which returns a new JunctionSeqCountSet.
Extends
Class "eSet", directly.
Class "VersionedBiobase", by class "eSet", distance 2.
Class "Versioned", by class "eSet", distance 3.
Note
End-users generally will not use any of these slots or methods directly.
However, they may be useful for model fit diagnostics and similar
statistical experimentation.
You can access method-mode information using the "AltMethods" attribute, and a list of all calls using the "callStack" attribute.
Author(s)
Stephen Hartley
See Also
The proper way to create a JunctionSeqCountSet is to use readJunctionSeqCounts or
runJunctionSeqAnalyses.
Examples
showClass("JunctionSeqCountSet")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(JunctionSeq)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
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: GenomeInfoDb
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")'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/JunctionSeq/JunctionSeqCountSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: JunctionSeqCountSet-class
> ### Title: Class '"JunctionSeqCountSet"'
> ### Aliases: JunctionSeqCountSet-class JunctionSeqCountSet
> ### Keywords: classes
>
> ### ** Examples
>
> showClass("JunctionSeqCountSet")
Class "JunctionSeqCountSet" [package "JunctionSeq"]
Slots:
Name: designColumns dispFitCoefs
Class: character numeric
Name: fittedMu dispFunctionType
Class: matrix list
Name: dispFunction dispFunctionJct
Class: function function
Name: dispFunctionExon formulas
Class: function list
Name: annotationFile geneCountData
Class: character matrix
Name: countVectors altSizeFactors
Class: matrix data.frame
Name: plottingEstimates plottingEstimatesVST
Class: list list
Name: geneLevelPlottingEstimates modelFitForHypothesisTest
Class: list list
Name: modelFitForEffectSize flatGffData
Class: list data.frame
Name: flatGffGeneData analysisType
Class: list character
Name: DESeqDataSet modelCoefficientsSample
Class: DESeqDataSet list
Name: modelCoefficientsGene assayData
Class: list AssayData
Name: phenoData featureData
Class: AnnotatedDataFrame AnnotatedDataFrame
Name: experimentData annotation
Class: MIAxE character
Name: protocolData .__classVersion__
Class: AnnotatedDataFrame Versions
Extends:
Class "eSet", directly
Class "VersionedBiobase", by class "eSet", distance 2
Class "Versioned", by class "eSet", distance 3
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.