Package 'cummeRbund'

Description

Allows for persistent storage, access, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations. ~~ A concise (1-5 lines) description of the package ~~

Details

Index:

CuffData-class          Class "CuffData"
CuffDist-class          Class "CuffDist"
CuffFeature-class       Class "CuffFeature"
CuffFeatureSet-class    Class "CuffFeatureSet"
CuffGene-class          Class "CuffGene"
CuffGeneSet-class       Class "CuffGeneSet"
CuffSet-class           Class "CuffSet"
JSdist                  Jensen-Shannon distance on columns
addFeatures             addFeatures
addFeatures-methods     ~~ Methods for Function addFeatures in Package
                        'cummeRbund' ~~
createDB                createDB
csBoxplot               csBoxplot
csBoxplot-methods       ~~ Methods for Function csBoxplot in Package
                        'cummeRbund' ~~
csDensity               Density plot of CuffData
csDensity-methods       ~~ Methods for Function csDensity in Package
                        'cummeRbund' ~~
csHeatmap               csHeatmap
csHeatmap-methods       ~~ Methods for Function csHeatmap in Package
                        'cummeRbund' ~~
csScatter               Scatter Plot
csScatter-methods       ~~ Methods for Function csScatter in Package
                        'cummeRbund' ~~
csVolcano               Volcano Plot
csVolcano-methods       ~~ Methods for Function csVolcano in Package
                        'cummeRbund' ~~
cummeRbund-package      cummeRbund: The finishing touch on your Tuxedo
                        workflow. Analysis, manipulation, and
                        visualization of Cufflinks HTS data.
diffData                Differential comparison data
diffData-methods        ~~ Methods for Function diffData in Package
                        'cummeRbund' ~~
dim-methods             ~~ Methods for Function dim in Package 'base'
                        ~~
expressionBarplot       Barplot
expressionBarplot-methods
                        ~~ Methods for Function expressionBarplot in
                        Package 'cummeRbund' ~~
expressionPlot          Expression Plot
expressionPlot-methods
                        ~~ Methods for Function expressionPlot in
                        Package 'cummeRbund' ~~
featureNames            Feature names
featureNames-methods    ~~ Methods for Function featureNames in Package
                        'cummeRbund' ~~
features                Features
features-methods        ~~ Methods for Function features in Package
                        'cummeRbund' ~~
fpkm                    Retrieve FPKM values
fpkm-methods            ~~ Methods for Function fpkm in Package
                        'cummeRbund' ~~
fpkmMatrix              Retrieve FPKM values as matrix
fpkmMatrix-methods      ~~ Methods for Function fpkmMatrix in Package
                        'cummeRbund' ~~
getGene                 getGene
getGene-methods         ~~ Methods for Function getGene in Package
                        'cummeRbund' ~~
getGenes                getGenes
getGenes-methods        ~~ Methods for Function getGenes in Package
                        'cummeRbund' ~~
getLevels               getLevels
getLevels-methods       ~~ Methods for Function getLevels in Package
                        'cummeRbund' ~~
length-methods          ~~ Methods for Function length in Package
                        'base' ~~
makeprobs               Transform a matrix into probabilities by
                        columns
readCufflinks           readCufflinks
samples                 Get sample list from CuffData object
samples-methods         ~~ Methods for Function samples in Package
                        'cummeRbund' ~~
shannon.entropy         Shannon entropy

Further information is available in the following vignettes:

~~ An overview of how to use the package, including the most important ~~ ~~ functions ~~

Author(s)

L. Goff, C. Trapnell

Maintainer: Loyal A. Goff <[email protected]>

References

~~ Literature or other references for background information ~~

Description

Adds a data.frame of features to a the SQLite backend database.

Usage

## S4 method for signature 'CuffSet'
addFeatures(object, features, level="genes", ...)

Arguments

Details

None

Value

None

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

#None yet.

Description

Returns a data.frame from @count slot

Details

Returns a data.frame of count values.

Value

A data.frame of count-level values for a set of features.

Methods

signature(object = "CuffData")

signature(object = "CuffFeature")

signature(object = "CuffFeatureSet")

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

data(sampleData)
	count(PINK1)

Description

Retrieve count values as gene by condition matrix

Usage

## S4 method for signature 'CuffData'
countMatrix(object,fullnames=FALSE,sampleIdList)
## S4 method for signature 'CuffData'
repCountMatrix(object,fullnames=FALSE,repIdList)

Arguments

Details

None.

Value

A feature x condition matrix of count values.

Note

None

Author(s)

Loyal A. Goff

References

None.

Examples

data(sampleData)
	countMatrix(sampleGeneSet)
	repCountMatrix(sampleGeneSet)

Description

Creates a ggplot2 plot object with a geom_box layer displaying summary statistics for FPKM values across samples (x).

Usage

## S4 method for signature 'CuffData'
csBoxplot(object, logMode=TRUE, pseudocount=0.0001, replicates=FALSE,...)

Arguments

Details

None

Value

A ggplot2 plot object with a geom_box layer.

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data and create CuffSet object
	genes<-a@genes #CuffData object for all genes
	csBoxplot(genes)

Description

Returns a ggplot2 plot object with geom_line layer plotting FPKM values over conditions faceted by k-means clustering clusters. (Euclidean). This is very crude at this point. This does not return any of the clustering information directly, but if you want it, you can retrieve it from the ggplot object returned.

Usage

## S4 method for signature 'CuffFeatureSet'
csCluster(object,k,logMode=T,method = "none",pseudocount=1,...)

Arguments

Details

Uses 'kmeans' function.

Author(s)

Loyal A. Goff

Source

None

References

None.

Examples

data(sampleData)
	csCluster(sampleGeneSet,4)

Description

Replaces the default plotting behavior of the old csCluster. Takes as an argument the output of csCluster and plots expression profiles of features facet by cluster.

Usage

csClusterPlot(clustering, pseudocount=1.0,logMode=FALSE,drawSummary=TRUE,sumFun=mean_cl_boot)

Arguments

Details

This replaces the default plotting behavior of the old csCluster() method. This was necessary so as to preserve the cluster information obtained by csCluster in a stable format. The output of csClusterPlot is a ggplot2 object of expressionProfiles faceted by cluster ID.

Value

A ggplot2 object of expressionProfiles faceted by cluster ID.

Note

None.

Author(s)

Loyal A. Goff

References

None.

Examples

data(sampleData)
	myClustering<-csCluster(sampleGeneSet,k=4)
	csClusterPlot(myClustering)

Description

Creates a grid graphics plot of a dendrogram of Jensen-Shannon distances between conditions of a CuffFeatureSet or CuffGeneSet object.

Usage

## S4 method for signature 'CuffFeatureSet'
csDendro(object,logMode=T,pseudocount=1,replicates=FALSE)
## S4 method for signature 'CuffData'
csDendro(object,logMode=T,pseudocount=1,replicates=FALSE,...)

Arguments

Details

None

Value

Returns a dendrogram object and plots that object by default.

Note

None

Author(s)

Loyal A. Goff and Cole Trapnell

References

None.

Examples

data(sampleData)
	csDendro(sampleGeneSet)

Description

Creates a smoothed density plot, by sample, for log10 FPKM values from a cuffdiff run.

Usage

## S4 method for signature 'CuffData'
csDensity(object, logMode=TRUE, pseudocount=0, labels, features=FALSE, replicates=FALSE,...)
## S4 method for signature 'CuffFeatureSet'
csDensity(object, logMode=TRUE, pseudocount=0, labels, features=FALSE, replicates=FALSE,...)

Arguments

Details

Creates a density plot, by sample, for log10-transformed FPKM values from a cuffdiff run.

Value

A ggplot2 plot object

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data
	genes<-a@genes #Create CuffData object for all 'genes'
	d<-csDensity(genes) #Create csDensity plot
	d #Render plot

Description

Creates a ggplot plot object with a geom_tile layer of JS Distance values between samples or genes.

Usage

## S4 method for signature 'CuffFeatureSet'
csDistHeat(object, replicates=F, samples.not.genes=T,
  logMode=T, pseudocount=1.0,
  heatscale=c(low='lightyellow',mid='orange',high='darkred'),
  heatMidpoint=NULL, ...)

Arguments

Details

None

Value

A ggplot2 plot object with a geom_tile layer to display distance between samples or genes.

Note

None

Author(s)

Loyal A. Goff, Cole Trapnell, and David Kelley

References

None

Examples

data(sampleData)
	csDistHeat(sampleGeneSet)

Description

Creates a ggplot plot object with a geom_tile layer of FPKM values per feature and sample.

Usage

## S4 method for signature 'CuffFeatureSet'
csHeatmap(object, rescaling='none', clustering='none', labCol=T, labRow=T, logMode=T, pseudocount=1.0, 
		border=FALSE, heatscale= c(low='lightyellow',mid='orange',high='darkred'), heatMidpoint=NULL, fullnames = T, replicates=FALSE,method='none', ...)
## S4 method for signature 'CuffFeatureSet'
csFoldChangeHeatmap(object, control_condition, replicate_num=NULL, clustering='none', labCol=T, labRow=T, logMode=F, pseudocount=1.0, 
		border=FALSE, heatscale=c(low='steelblue',mid='white',high='tomato'), heatMidpoint=0,fullnames=T,replicates=FALSE,method='none',heatRange=3, ...)

Arguments

Details

None

Value

A ggplot2 plot object with a geom_tile layer to display FPKM values by sample (x) and feature (y)

Note

None

Author(s)

Loyal A. Goff and Cole Trapnell

References

None.

Examples

data(sampleData)
	csHeatmap(sampleGeneSet)

Description

A scatter plot comparing the FPKM values from two samples in a cuffdiff run.

Usage

## S4 method for signature 'CuffData'
csScatter(object, x, y, logMode=TRUE, pseudocount=1.0, labels, smooth=FALSE, colorByStatus = FALSE, drawRug=TRUE, ...)
## S4 method for signature 'CuffData'
csScatterMatrix(object,replicates=FALSE,logMode=TRUE,pseudocount=1.0, hexbin=FALSE, useCounts=FALSE, ...)

Arguments

Details

None

Value

ggplot object with geom_point and geom_rug layers

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data
	genes<-a@genes #Create CuffData object for all genes
	s<-csScatter(genes,'hESC','Fibroblasts',smooth=TRUE) #Create plot object
	s #render plot object

Description

Returns a matrix of 'Specificity scores' (S) defined as 1-JSD(p_g,q_i) where p_g is the Log10+1 expression profile of a gene g across all conditions j, collapsed into a probability distribution, and q_i is the unit vector of 'perfect expression' in a given condition i.

Usage

## S4 method for signature 'CuffFeatureSet'
csSpecificity(object,logMode=T,pseudocount=1,relative=FALSE,...)
## S4 method for signature 'CuffData'
csSpecificity(object,logMode=T,pseudocount=1,relative=FALSE,...)

Arguments

Details

None

Author(s)

Loyal A. Goff

Source

None

References

None.

Examples

data(sampleData)
	csSpecificity(sampleGeneSet)

Description

Creates a volcano plot of log fold change in expression vs -log(pval) for a pair of samples (x,y)

Usage

## S4 method for signature 'CuffData'
csVolcano(object, x, y, alpha=0.05, showSignificant=TRUE,features=FALSE, xlimits = c(-20, 20), ...)
## S4 method for signature 'CuffData'
csVolcanoMatrix(object,alpha=0.05,xlimits=c(-20,20),mapping=aes(),...)

Arguments

Details

This creates a 'volcano' plot of fold change vs. significance for a pairwise comparison of genes or features across two different samples.

Value

A ggplot2 plot object

Note

None

Author(s)

Loyal A. Goff

References

None.

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object
genes<-a@genes #Create cuffData object for all genes
v<-csVolcano(genes,"hESC","Fibroblasts") # Volcano plot of all genes for conditions x='hESC' and y='Fibroblast'
v #print plot

Description

A 'pointer' class for all information (FPKM, annotation, differential expression) for a given feature type (genes, isoforms, TSS, CDS). The methods for this function communicate directly with the SQL backend to present data to the user.

Objects from the Class

Objects can be created by calls of the form new("CuffData", DB, tables, filters, type, idField, ...).

Slots

DB:

Object of class "SQLiteConnection" ~~

tables:

Object of class "list" ~~

filters:

Object of class "list" ~~

type:

Object of class "character" ~~

idField:

Object of class "character" ~~

Methods

dim

signature(x = "CuffData"): ...

getFeatures

signature(object = "CuffData"): ...

DB

signature(object = "CuffData"): Accessor for @DB slot

diffTable

signature(object = "CuffData"): Create a Full table (wide format) of differential expression information for all pairwise comparisons

makeRnk

signature(object = "CuffData"): Internal method to create .rnk file. Should not be called directly

annotation

signature(object="CuffData"): Access annotation data

Note

None

Author(s)

Loyal A. Goff

References

None

See Also

None

Examples

showClass("CuffData")

Description

A 'pointer' class to information relative to the distribution-level tests (promoters, splicing, and relative CDS usage)

Objects from the Class

Objects can be created by calls of the form new("CuffDist", DB, table, type, idField, ...).

Slots

DB:

Object of class "SQLiteConnection" ~~

table:

Object of class "character" ~~

type:

Object of class "character" ~~

idField:

Object of class "character" ~~

Methods

dim

signature(x = "CuffDist"): ...

samples

signature(x = "CuffDist"): ...

DB

signature(object = "CuffDist"): Accessor for @DB slot

Note

None

Author(s)

Loyal A. Goff

References

None

See Also

None

Examples

showClass("CuffDist")

Description

A 'data' container class for all FPKM, annotation, and differential expression data for a single feature (gene, isoform, TSS, or CDS).

Objects from the Class

Objects can be created by calls of the form new("CuffFeature", annotation, fpkm, diff, ...).

Slots

annotation:

Object of class "data.frame" ~~

fpkm:

Object of class "data.frame" ~~

diff:

Object of class "data.frame" ~~

repFpkm:

Object of class "data.frame" ~~

count:

Object of class "data.frame" ~~

genome:

Object of class "character" ~~

Methods

fpkmMatrix

signature(object="CuffFeature"): ...

repFpkmMatrix

signature(object = "CuffFeature"): ...

length

signature(x = "CuffFeature"): ...

Accessors

annotation

signature(object="CuffFeature"): Access @annotation slot

diffData

signature(object="CuffFeature"): Access @diff slot

samples

signature(object="CuffFeature"): Get vector of samples

Note

'CuffGene' is a superclass of 'CuffFeature' that links gene information for a given gene with all isoform-, TSS-, and CDS-level data for the given gene.

Author(s)

Loyal A. Goff

References

None

See Also

CuffGene

Examples

showClass("CuffFeature")

Description

A 'data' container class for all FPKM, annotation, and differential expression data for a set of features (genes, isoforms, TSS, CDS).

Objects from the Class

Objects can be created by calls of the form new("CuffFeatureSet", annotation, fpkm, diff, ...).

Slots

annotation:

Object of class "data.frame" ~~

fpkm:

Object of class "data.frame" ~~

diff:

Object of class "data.frame" ~~

repFpkm:

Object of class "data.frame" ~~

count:

Object of class "data.frame" ~~

genome:

Object of class "character" ~~

Methods

diffData

signature(object = "CuffFeatureSet"): ...

featureNames

signature(object = "CuffFeatureSet"): ...

features

signature(object = "CuffFeatureSet"): ...

fpkmMatrix

signature(object = "CuffFeatureSet"): ...

repFpkmMatrix

signature(object = "CuffFeatureSet"): ...

countMatrix

signature(object = "CuffFeatureSet"): ...

samples

signature(object = "CuffFeatureSet"): ...

length

signature(object = "CuffFeatureSet"): ...

Accessors

annotation

signature(object="CuffFeatureSet"): Access @annotation slot

Note

None.

Author(s)

Loyal A. Goff

References

None.

See Also

CuffGeneSet

Examples

showClass("CuffFeatureSet")

Description

A 'data' container class for all FPKM, annotation, and differential expression Data (as well as for all linked features) for a given gene.

Objects from the Class

Objects can be created by calls of the form new("CuffGene", id, isoforms, TSS, CDS, promoters, splicing, relCDS, annotation, fpkm, diff, ...).

Slots

id:

Object of class "character" ~~

isoforms:

Object of class "CuffFeature" ~~

TSS:

Object of class "CuffFeature" ~~

CDS:

Object of class "CuffFeature" ~~

promoters:

Object of class "CuffFeature" ~~

relCDS:

Object of class "CuffFeature" ~~

splicing:

Object of class "CuffFeature" ~~

annotation:

Object of class "data.frame" ~~

genome:

Object of class "character" ~~

fpkm:

Object of class "data.frame" ~~

diff:

Object of class "data.frame" ~~

features:

Object of class "data.frame" ~~

Extends

Class "CuffFeature", directly.

Methods

length

signature(object="CuffFeature"): Part of length validation (internal use only)

makeGeneRegionTrack

signature(object="CuffFeature"): Creates a GeneRegionTrack object (see package Gviz) from a CuffGene object.

genePlot

signature(object="CuffFeature"): Internal use only.

csPie

signature(object="CuffGene"): Allows for visualization of relative isoform proportion as a pie chart by condition (or optionally as stacked bar charts by adding + coord_cartesian()

Accessors

genes

signature(object = "CuffGene"): Access @genes slot

isoforms

signature(object = "CuffGene"): Access @isoforms slot

TSS

signature(object = "CuffGene"): Access @TSS slot

CDS

signature(object = "CuffGene"): Access @CDS slot

promoters

signature(object = "CuffGene"): Access @CDS slot

relCDS

signature(object = "CuffGene"): Access @CDS slot

splicing

signature(object = "CuffGene"): Access @CDS slot

features

signature(object = "CuffGene"): Access @features slot

Note

None.

Author(s)

Loyal A. Goff

References

None.

See Also

CuffFeature

Examples

showClass("CuffGene")

Description

A 'data' container class for all FPKM, annotation, and differential expression data (an associated features) for a given set of genes.

Objects from the Class

Objects can be created by calls of the form new("CuffGeneSet", annotation, fpkm, diff, ...).

Slots

ids:

Object of class "character" ~~

isoforms:

Object of class "CuffFeatureSet" ~~

TSS:

Object of class "CuffFeatureSet" ~~

CDS:

Object of class "CuffFeatureSet" ~~

promoters:

Object of class "CuffFeatureSet" ~~

relCDS:

Object of class "CuffFeatureSet" ~~

splicing:

Object of class "CuffFeatureSet" ~~

annotation:

Object of class "data.frame" ~~

fpkm:

Object of class "data.frame" ~~

diff:

Object of class "data.frame" ~~

Extends

Class "CuffFeatureSet", directly.

Methods

No methods defined with class "CuffGeneSet" in the signature.

Accessors

genes

signature(object = "CuffGeneSet"): Access @genes slot

isoforms

signature(object = "CuffGeneSet"): Access @isoforms slot

TSS

signature(object = "CuffGeneSet"): Access @TSS slot

CDS

signature(object = "CuffGeneSet"): Access @CDS slot

promoters

signature(object = "CuffGeneSet"): Access @promoters slot

relCDS

signature(object = "CuffGeneSet"): Access @relCDS slot

splicing

signature(object = "CuffGeneSet"): Access @splicing slot

Note

None.

Author(s)

Loyal A. Goff

References

None.

See Also

CuffFeatureSet

Examples

showClass("CuffGeneSet")

Description

A 'pointer' class to connect to, and retrieve data from the SQLite backend database.

Objects from the Class

Objects can be created by calls of the form new("CuffSet", DB, conditions, genes, isoforms, TSS, CDS, promoters, splicing, relCDS, ...). Available methods are primary accessors to retrieve CuffGeneSet or CuffGene objects for manipulation.

Slots

DB:

Object of class "SQLiteConnection" ~~

conditions:

Object of class "data.frame" ~~

genes:

Object of class "CuffData" ~~

isoforms:

Object of class "CuffData" ~~

phenoData:

Object of class "data.frame" ~~

TSS:

Object of class "CuffData" ~~

CDS:

Object of class "CuffData" ~~

promoters:

Object of class "CuffDist" ~~

splicing:

Object of class "CuffDist" ~~

relCDS:

Object of class "CuffDist" ~~

conditions:

Object of class "data.frame" ~~

Methods

[

signature(x = "CuffSet"): ...

Accessors

DB

signature(object="CuffSet"): Access @DB slot

genes

signature(object = "CuffSet"): Access @genes slot

isoforms

signature(object = "CuffSet"): Access @isoforms slot

TSS

signature(object = "CuffSet"): Access @TSS slot

CDS

signature(object = "CuffSet"): Access @CDS slot

promoters

signature(object = "CuffSet"): Access @promoters slot

splicing

signature(object = "CuffSet"): Access @splicing slot

relCDS

signature(object = "CuffSet"): Access @relCDS slot

varModel

signature(object = "CuffSet"): Access varModel info

Note

None.

Author(s)

Loyal A. Goff

References

None.

See Also

None.

Examples

showClass("CuffSet")

Description

An accessor method to retrieve differential expression data from a 'CuffData', 'CuffFeatureSet', or 'CuffFeature' object

Usage

## S4 method for signature 'CuffData'
diffData(object, x, y, features=FALSE)
## S4 method for signature 'CuffData'
diffTable(object,logCutoffValue=99999)

Arguments

Details

None

Value

A data.frame object

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

data(sampleData)
	diff<-diffData(sampleGeneSet) #returns a dataframe of differential expression data from sample CuffGeneSet object.

Description

Dimensionality reduction plots for feature selection and extraction for cummeRbund

Usage

## S4 method for signature 'CuffData'
MDSplot(object,replicates=FALSE,logMode=TRUE,pseudocount=1.0)
## S4 method for signature 'CuffData'
PCAplot(object,x="PC1", y="PC2",replicates=FALSE,pseudocount=1.0,scale=TRUE,showPoints = TRUE,...)

Arguments

Details

These methods attempt to project a matrix of expression estimates across conditions and/or replicates onto a smaller number of dimesions for feature selection, feature extraction, and can also be useful for outlier detection.

Value

A ggplot2 object.

Note

None.

Author(s)

Loyal A. Goff

References

None.

Examples

cuff<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data
	p<-PCAplot(genes(cuff),x="PC2",y="PC3",replicates=TRUE)
	m<-MDSplot(genes(cuff),replicates=TRUE)
	p #Render PCA plot
	m #Render MDS plot

Description

A scatter plot comparing the mean counts against the estimated dispersion for a given level of features from a cuffdiff run.

Usage

## S4 method for signature 'CuffData'
dispersionPlot(object)
## S4 method for signature 'CuffSet'
dispersionPlot(object)

Arguments

Details

None

Value

ggplot object with geom_point layer

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data
	genes<-genes(a) #Create CuffData object for all genes
	d<-dispersionPlot(genes) #Create plot object
	d #render plot object

Description

Returns a data.frame of distribution-level test values from a CuffDist object (@promoters, @splicing, @relCDS)

Usage

## S4 method for signature 'CuffDist'
distValues(object)

Arguments

Details

None

Value

Returns a data.frame of distribution-level test values.

Note

None

Author(s)

Loyal A. Goff

References

None

See Also

None

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) # Read cufflinks data and create CuffSet object
	distValues(a@promoters) # returns data.frame of values from CuffDist object in slot 'promoters'

Description

Exploratory analysis methods for cummeRbund RNA-Seq data.

Usage

## S4 method for signature 'CuffData'
csNMF(object,k,logMode=T,pseudocount=1,maxiter=1000,replicates=FALSE,fullnames=FALSE)
## S4 method for signature 'CuffFeatureSet'
csNMF(object,k,logMode=T,pseudocount=1,maxiter=1000,replicates=FALSE,fullnames=FALSE)

Arguments

Details

csNMF is a convenience method to invoke the nnmf() method from package:NMFN. This performs non-negative matrix factorization on the provided data and can be useful for many downstream applications.

Value

csNMF returns W, H - decomposed matrices of input FPKM values. (See package:NMFN for details)

Note

None.

Author(s)

Loyal A. Goff

References

None.

Examples

data(sampleData)
	csNMF(sampleGeneSet,4)

Description

A barplot of FPKM values with confidence intervals for a given gene, set of genes, or features of a gene (e.g. isoforms, TSS, CDS, etc).

Usage

## S4 method for signature 'CuffFeatureSet'
expressionBarplot(object, logMode=TRUE, pseudocount=1.0, showErrorbars=TRUE, showStatus=TRUE, replicates=FALSE, ...)

Arguments

Details

None

Value

A ggplot2 plot object

Note

Need to implement logMode and features for this plotting method.

Author(s)

Loyal A. Goff

References

None

Examples

data(sampleData)
	PINK1 # sample CuffFeature object
	expressionBarplot(PINK1) #Barplot of PINK1 FPKM values
	expressionBarplot(PINK1@isoforms) #Barplot of PINK1 FPKM values faceted by isoforms

Description

A line plot (optionally with confidence intervals) detailing FPKM expression levels across conditions for a given gene(s) or feature(s)

Usage

## S4 method for signature 'CuffFeature'
expressionPlot(object, logMode=FALSE, pseudocount=1.0, drawSummary=FALSE, sumFun=mean_cl_boot, showErrorbars=TRUE, showStatus=TRUE, replicates=FALSE, facet = TRUE,...)

Arguments

Details

None

Value

A ggplot2 plot object

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

data(sampleData)
	PINK1 # sample CuffFeature object
	expressionPlot(PINK1) #Line plot of PINK1 FPKM values
	expressionPlot(PINK1@isoforms) #Line plot of PINK1 FPKM values faceted by isoforms

Description

Retrive a vector of feature names from a 'CuffData' or 'CuffFeatureSet' object

Usage

## S4 method for signature 'CuffData'
featureNames(object)

Arguments

Details

None

Value

A list of feature names

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

data(sampleData)
featureNames(sampleGeneSet)

Description

Returns a data frame of features from a CuffGene object

Usage

## S4 method for signature 'CuffGene'
features(object)

Arguments

Details

None

Value

A data.frame of feature-level information

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

data(sampleData)
	features(PINK1)

Description

A helper function to retrieve the gene_ids given a 'lookup' value (e.g. gene_short_name, isoform_id, etc). Utility to search for gene_id and gene_short_name given a single 'query' string (e.g. query='pink1' will return all genes with 'pink1' (case-insensitive) in the gene_short_name field.

Usage

## S4 method for signature 'CuffSet'
findGene(object, query)

Arguments

Details

None.

Value

Returns a data.frame of gene_id and gene_short_name values corresponding to genes from which 'query' matches

Note

Right now, this does not return an error if it cannot find a gene. (this is probably a bad thing...)

Author(s)

Loyal A. Goff

References

None.

Examples

cuff<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data and create master CuffSet object
	myQuery<-'pink1'
	findGene(cuff,myQuery) # Retrieve gene_id values for any genes matching 'pink1'

Description

Returns a CuffGeneSet containing n genes with the most similar expression profiles to gene/profile x.

Usage

## S4 method for signature 'CuffSet'
findSimilar(object, x, n,distThresh,returnGeneSet=TRUE,...)

Arguments

Details

By default, returns a CuffGeneSet object with n similar genes. This may change in the future.

Value

A CuffGeneSet object of n most similar genes to x.

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund"))
	mySimilarGenes<-findSimilar(a,"PINK1",10)

Description

Returns a data.frame from @FPKM slot

Details

Returns a data.frame of FPKM values.

Value

A data.frame of FPKM-level values for a set of features.

Methods

signature(object = "CuffData")

signature(object = "CuffFeature")

signature(object = "CuffFeatureSet")

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

data(sampleData)
	fpkm(PINK1)

Description

Retrieve FPKM values as gene by condition (fpkmMatrix) or gene by replicate (repFpkmMatrix) matrix

Usage

## S4 method for signature 'CuffData'
fpkmMatrix(object,fullnames=FALSE,sampleIdList)
## S4 method for signature 'CuffData'
repFpkmMatrix(object,fullnames=FALSE,repIdList)

Arguments

Details

None.

Value

A feature x condition matrix of FPKM values.

Note

None

Author(s)

Loyal A. Goff

References

None.

Examples

data(sampleData)
	fpkmMatrix(sampleGeneSet)
	repFpkmMatrix(sampleGeneSet)

Description

Primary accessor from a CuffSet object to retrieve all related information for >1 (MANY) given FEATURES, indexed by tracking id.

Usage

## S4 method for signature 'CuffSet'
getFeatures(object, featureIdList, sampleIdList=NULL,level='isoforms')

Arguments

Details

None.

Value

Returns a CuffFeatureSet object containing all related information for a given set of tracking_id values

Note

Right now, this does not return an error if it cannot find a gene. (this is probably a bad thing...)

Author(s)

Loyal A. Goff

References

None.

Examples

cuff<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data and create master CuffSet object
	sample.isoform.ids<-sample(featureNames(isoforms(cuff)),10)
	myGene<-getFeatures(cuff,sample.isoform.ids) # Retrieve all information for a set of 10 sampled features.

Description

Primary accessor from a CuffSet object to retrive all related information for 1 (one) given gene, indexed by gene_id or gene_short_name.

Usage

## S4 method for signature 'CuffSet'
getGene(object, geneId, sampleIdList=NULL)

Arguments

Details

None.

Value

Returns a CuffGene object containing all related information for a given gene_id or gene_short_name

Note

Right now, this does not return an error if it cannot find a gene. (this is probably a bad thing...)

Author(s)

Loyal A. Goff

References

None.

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data and create master CuffSet object
	myGene<-getGene(a,"PINK1") # Retrieve all information for gene "PINK1"

Description

A helper function to retrieve the gene_ids for a given list of feature ids (e.g. isoform_ids, tss_group_ids, or CDS_ids). This should not be called directly by the user

Usage

## S4 method for signature 'CuffSet'
getGeneId(object, idList)

Arguments

Details

None.

Value

Returns a vector of gene_id values corresponding to genes from which idList are sub-features.

Note

Right now, this does not return an error if it cannot find a gene. (this is probably a bad thing...)

Author(s)

Loyal A. Goff

References

None.

Examples

cuff<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data and create master CuffSet object
	sampleFeatureIds<-sample(featureNames(isoforms(cuff)),10)
	correspondingGeneIds<-getGeneId(cuff,sampleFeatureIds) # Retrieve gene_id values for parent genes of sampleFeatureIds.

Description

Primary accessor from a CuffSet object to retrive all related information for >1 (MANY) given genes, indexed by gene_id or gene_short_name.

Usage

## S4 method for signature 'CuffSet'
getGenes(object, geneIdList, sampleIdList=NULL)

Arguments

Details

None.

Value

Returns a CuffGeneSet object containing all related information for a given set of gene_id or gene_short_name values

Note

Right now, this does not return an error if it cannot find a gene. (this is probably a bad thing...)

Author(s)

Loyal A. Goff

References

None.

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data and create master CuffSet object
	data(sampleData)
	sampleIDs
	myGene<-getGenes(a,sampleIDs) # Retrieve all information for a set of 20 'sample' genes.

Description

Returns a list of samples as levels. This should not be called directly by user.

Usage

## S4 method for signature 'CuffData'
getLevels(object)

Arguments

Details

For internal usage only.

Value

A vector of sample names as factors.

Note

None.

Author(s)

Loyal A. Goff

References

None.

Description

Returns a list of replicate samples as levels. This should not be called directly by user.

Usage

## S4 method for signature 'CuffData'
getRepLevels(object)

Arguments

Details

For internal usage only.

Value

A vector of replicate names as factors.

Note

None.

Author(s)

Loyal A. Goff

References

None.

Description

Returns the identifiers of significant genes in a vector format.

Usage

## S4 method for signature 'CuffSet'
getSig(object,x,y,alpha=0.05,level='genes',method="BH", useCuffMTC=FALSE)

Arguments

Details

This is a convenience function to quickly retrieve vectors of identifiers for genes or features that were determined to be significantly regulated between conditions by cuffdiff. This function only returns tracking IDs that correspond to tests with an 'OK' status from cuffdiff, NOTEST values are ignored. By default getSig returns a vector of IDs for all pairwise comparisons together. If you specify an 'x' AND 'y' values as sample names, then only the features that are significant in that particular pairwise comparison are reported, after appropriate multiple testing correction of output p-values.

Value

A vector of feature IDs.

Note

None.

Author(s)

Loyal A. Goff

References

None.

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data in sample directory and creates CuffSet object 'a'
	mySig<-getSig(a,x='hESC',y='Fibroblasts',alpha=0.05,level='genes')
	head(mySig)

Description

Returns the identifiers of significant genes in a test table - like format.

Usage

## S4 method for signature 'CuffSet'
getSigTable(object,alpha=0.05,level='genes')

Arguments

Details

This is a convenience function to quickly retrieve lists of identifiers for genes or features that were determined to be significantly regulated between conditions by cuffdiff. This function only returns tracking IDs that correspond to tests with an 'OK' status from cuffdiff, NOTEST values are ignored or reported as NA. By default getSig returns a table of genes x conditions, where the column names represent the pairwise comparisons from the cuffdiff analysis. The values in the table are 1 for features that are significant for this comparison and 0 for genes that are not, any failed tests are reported as <NA>.Only includes the features that are significant in at least one comparison.

Value

A data.frame of pairwise test results.

Note

None.

Author(s)

Loyal A. Goff

References

None.

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data in sample directory and creates CuffSet object 'a'
	mySigTable<-getSigTable(a,alpha=0.05,level='genes')
	head(mySigTable)

Description

JSdist takes a matrix of expression probabilites (calculated directly or output from makeprobs()) and returns a dist object of the pairwise Jensen-Shannon distances between columns

Usage

JSdist(mat,...)

Arguments

Details

Returns pairwise Jensen-Shannon distance (in the form of a dist object) for a matrix of probabilities (by column)

Value

A dist object of pairwise J-S distances between columns.

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

mat<-matrix(sample(1:50,50),10)
probs<-makeprobs(mat)
js.distance<-JSdist(probs)

Description

JSdist takes a matrix of expression probabilites (calculated directly or output from makeprobs()) and returns a matrix of Jensen-Shannon distances between individual rows and a specific vector of probabilities (q)

Usage

JSdistFromP(mat,q)

Arguments

Details

Returns Jensen-Shannon distance for each row of a matrix of probabilities against a provided probability distribution (q)

Value

A vector of JS distances

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

mat<-matrix(sample(1:50,50),10)
q<-c(100,4,72,8,19)
q<-q/sum(q)
js.distance<-JSdistFromP(mat,q)

Description

Returns the Jensen-Shannon Distance (square root of JS divergence) between two probability vectors.

Usage

JSdistVec(p, q)

Arguments

Details

Should not be called directly by user.

Value

Returns the JS distance as a numeric

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

p<-sample(1:5000,20)
	q<-sample(1:5000,20)
	p<-makeprobsvec(p)
	q<-makeprobsvec(q)
	JSdistVec(p,q)

Description

This function takes a matrix of expression values (must be greater than 0) and returns a matrix of probabilities by column. This is a required transformation for the Jensen-Shannon distance which is a metric that operates on probabilities.

Usage

makeprobs(a)

Arguments

Details

To make a matrix of probabilities by row, use t() to transpose prior to calling makeprobs.

Value

A matrix of expression probabilities by column.

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

myMat<-matrix(sample(1:50,50),10)
probs<-makeprobs(myMat)

Description

Sums a vector of numerics and divides by the sum

Usage

makeprobsvec(p)

Arguments

Details

None

Value

A vector of probabilities

Note

Should not be called directly by user.

Author(s)

Loyal A. Goff

References

None

Examples

p<-sample(1:5000,20)
	makeprobsvec(p)

Description

Creates an M vs A plot (Avg intensity vs log ratio) for a given pair of conditions across all fpkms

Usage

## S4 method for signature 'CuffData'
MAplot(object,x,y,logMode=T,pseudocount=1,smooth=FALSE,useCount=FALSE)

Arguments

Details

None

Value

Returns a ggplot MvsA plot object.

Note

None

Author(s)

Loyal A. Goff and Cole Trapnell

References

None.

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data
	genes<-a@genes #Create CuffData object for all 'genes'
	d<-MAplot(genes,'hESC','Fibroblasts') #Create csDensity plot
	d #Render plot

Description

A sample 'CuffGene' dataset

Usage

data(sampleData)

Format

PINK1 is a CuffGene object (extends CuffFeature) with all sample gene-, isoform-, TSS-, and CDS-level data for the gene 'PINK1'.

Details

Sample CuffGene data for gene 'PINK1'

Source

None

References

None

Examples

data(sampleData)
PINK1

Description

A collection of ggplot2 visualizations for quality control assessment of cuffdiff output.

- fpkmSCVPlot: A measure of cross-replicate variability, the squared coefficient of variation is a normalized measure of variance between empirical repicate FPKM values per condition, across the range of FPKM estimates.

Usage

## S4 method for signature 'CuffData'
fpkmSCVPlot(object,FPKMLowerBound=1, showPool = FALSE)

Arguments

Details

None

Value

A ggplot2 plot object with a geom_box layer.

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data and create CuffSet object
	genes<-a@genes #CuffData object for all genes
	csBoxplot(genes)

Description

This initializes the backend SQLite table and provides a DB connection for all downstream data analysis.

Usage

readCufflinks(dir = getwd(), dbFile = "cuffData.db", gtfFile = NULL, 
				runInfoFile = "run.info", repTableFile = "read_groups.info",
				geneFPKM = "genes.fpkm_tracking", geneDiff = "gene_exp.diff", geneCount="genes.count_tracking", geneRep="genes.read_group_tracking",
				isoformFPKM = "isoforms.fpkm_tracking", isoformDiff = "isoform_exp.diff", isoformCount="isoforms.count_tracking", isoformRep="isoforms.read_group_tracking",
				TSSFPKM = "tss_groups.fpkm_tracking", TSSDiff = "tss_group_exp.diff", TSSCount="tss_groups.count_tracking", TSSRep="tss_groups.read_group_tracking",
				CDSFPKM = "cds.fpkm_tracking", CDSExpDiff = "cds_exp.diff", CDSCount="cds.count_tracking", CDSRep="cds.read_group_tracking",
				CDSDiff = "cds.diff",
				promoterFile = "promoters.diff", 
				splicingFile = "splicing.diff",
				varModelFile = "var_model.info",
				driver = "SQLite", 
				genome = NULL, 
				rebuild = FALSE,verbose=FALSE, ...)

Arguments

Details

This is the initialization function for the cummeRbund package. It creates the SQLite backend database, populates the data, and provides a connection object for all future interactions with the dataset. Once the initial build is complete, this function will default to using the database for all future sessions. IMPORTANT: - Each R session should begin with a call to readCufflinks to re-open the connection to the database. - Should any connectivity issues to the database arise, another call to readCufflinks should create a new connection object and repair any issue. - The database can always be rebuild (using rebuild=TRUE) from the original CuffDiff output files.

Value

A CuffSet object. A 'pointer' class that allows interaction with cufflinks/cuffdiff data via a SQLite database backend.

Note

None.

Author(s)

Loyal A. Goff

References

None.

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data in sample directory and creates CuffSet object 'a'

Description

Returns a data.frame from @repFpkm slot

Details

Returns a data.frame of replicate FPKM values and associated statistics.

Value

A data.frame of replicate-level FPKM values and associated statistics for a set of features.

Methods

signature(object = "CuffData")

signature(object = "CuffFeature")

signature(object = "CuffFeatureSet")

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

data(sampleData)
	repFpkm(PINK1)

Description

Returns a list of replicate names from a CuffData or CuffFeatureSet object

Usage

## S4 method for signature 'CuffData'
replicates(object)

Arguments

Details

None

Value

A list of replicate sample names

Note

None

Author(s)

Loyal A. Goff

References

None

See Also

None

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object
	replicates(a@genes)

Description

Returns a data.frame of cuffdiff run parameters and information

Usage

## S4 method for signature 'CuffSet'
runInfo(object)

Arguments

Details

None

Value

A data.frame of run parameters

Note

None

Author(s)

Loyal A. Goff

References

None

See Also

None

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object
	runInfo(a)

Description

A sample CuffGeneSet data set for 20 genes.

Usage

data(sampleData)

Format

sampleGeneSet is a CuffGeneSet (extends CuffFeatureSet) object containing all sample gene-, isoform-, TSS-, and CDS-level data for 20 different genes. These data were derived from a toy set of hESC-vs-iPSC-vs-Fibroblast RNA-Seq expression data.

Details

None

Source

None

References

None

Examples

data(sampleData)

Description

A vector of gene_ids used to create 'sampleGeneSet' example

Usage

data(sampleData)

Format

The format is: chr "sampleIDs"

Details

None

Source

None

References

None

Examples

data(sampleData)

Description

Returns a list of sample names from a CuffData or CuffFeatureSet object

Usage

## S4 method for signature 'CuffData'
samples(object)

Arguments

Details

None

Value

A list of sample names

Note

None

Author(s)

Loyal A. Goff

References

None

See Also

None

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object
	samples(a@genes)

Description

Calculates the Shannon entropy for a probability distribution

Usage

shannon.entropy(p)

Arguments

Details

None

Value

Returns a numeric value for the Shannon entropy of the supplied probability distribution

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

x<-sample(1:500,50)
	p<-x/sum(x)
	shannon.entropy(p)

Description

Returns a ggplot2 plot object representing a matrix of significant features. This is a useful synopsis of all significant pairwise comparisons within the dataset.

Usage

## S4 method for signature 'CuffSet'
sigMatrix(object,alpha=0.05,level='genes',orderByDist=FALSE)

Arguments

Details

Creates a matrix plot to illustrate the number of significant features of type 'level' at a given alpha from a cuffdiff run.

Value

A ggplot2 plot object

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data
	d<-sigMatrix(a) #Create csDensity plot
	d #Render plot