CAGEset-class {CAGEr} | R Documentation

## Class `"CAGEset"`

### Description

This class is used to store one or more CAGE (Cap Analysis of Gene Expression) datasets in the form of TSSs derived from CAGE tags and frequency of their usage, and to store and extract all information generated during the workflow.

### Objects from the Class

Objects can be created by calls of the form `new("CAGEset", ...)`.
Objects of the class contain information on the genomic coordinates of TSSs derived from sequenced CAGE tags from multiple experiments, number of tags supporting each TSS in each experiment, normalized CAGE signal at each TSS, all information on specified parameters and results of all downstream analyses. Object has to be created before reading in the data by specifying input files and their type, referent genome and labels for individual CAGE datasets, as described in the vignette. Data is read by applying a function to a created object and all further slots are filled during the workflow by applying specific functions.

### Slots

`genomeName`:

  Object of class `"character"`: the name of the BSgenome package used as the referent genome

`inputFiles`:

  Object of class `"character"`: the paths to input files

`inputFilesType`:

  Object of class `"character"`: the type of input files (e.g. bam)

`sampleLabels`:

  Object of class `"character"`: the labels of individual CAGE experiments

`librarySizes`:

  Object of class `"integer"`: the total number of CAGE tags per experiment

`CTSScoordinates`:

  Object of class `"data.frame"`: the genomic coordinates of CAGE transcription start sites (CTSSs)

`tagCountMatrix`:

  Object of class `"data.frame"`: the number of CAGE tags supporting every CTSS in each experiment

`normalizedTpmMatrix`:

  Object of class `"data.frame"`: the normalized CAGE signal supporting every CTSS in each experiment

`CTSSexpressionClusteringMethod`:

  Object of class `"character"`: the method used for expression clustering of CTSSs

`CTSSexpressionClasses`:

  Object of class `"character"`: the labels of expression classes of CTSSs returned by expression clustering

`clusteringMethod`:

  Object of class `"character"`: the method used for clustering CTSSs into tag clusters (TC)

`filteredCTSSidx`:

  Object of class `"logical"`: the index of CTSSs included in tag clusters

`tagClusters`:

  Object of class `"list"`: the list of tag clusters per CAGE experiment

`CTSScumulativesTagClusters`:

  Object of class `"list"`: the cumulative distribution of CAGE signal along TCs

`tagClustersQuantileLow`:

  Object of class `"list"`: the positions of lower quantile(s) within TCs

`tagClustersQuantileUp`:

  Object of class `"list"`: the positions of upper quantile(s) within TCs

`consensusClusters`:

  Object of class `"data.frame"`: the genomic coordinates of consensus clusters created by aggregating TCs across experiments

`consensusClustersTpmMatrix`:

  Object of class `"matrix"` the normalized CAGE signal for every consensus cluster in each experiment

`consensusClustersExpressionClusteringMethod`:

  Object of class `"character"` the method used for expression clustering of consensus clusters

`consensusClustersExpressionClasses`:

  Object of class `"character"` the labels of expression classes of consensus clusters returned by expression clustering

`CTSScumulativesConsensusClusters`:

  Object of class `"list"` the cumulative distribution of CAGE signal along consensus clusters

`consensusClustersQuantileLow`:

  Object of class `"list"` the positions of lower quantile(s) within consensus clusters

`consensusClustersQuantileUp`:

  Object of class `"list"` the positions of upper quantile(s) within consensus clusters

`shiftingGroupX`:

  Object of class `"character"` the label(s) of experiment(s) in the first shifting group

`shiftingGroupY`:

  Object of class `"character"` the label(s) of experiment(s) in the second shifting group

`consensusClustersShiftingScores`:

  Object of class `"data.frame"` the shifting scores and P-values/FDR for comparison of consensus clusters between two (groups of) experiments

### Methods

CTSSclusteringMethod

  `signature(object = "CAGEset")`: extracts the method used for clustering CTSSs into tag clusters (TC)

CTSScoordinates

  `signature(object = "CAGEset")`: extracts the genomic coordinates of all CTSSs

CTSSnormalizedTpm

  `signature(object = "CAGEset")`: extracts the normalized CAGE signal supporting every CTSS in each experiment

CTSStagCount

  `signature(object = "CAGEset")`: extracts the number of CAGE tags supporting every CTSS in each experiment

aggregateTagClusters

  `signature(object = "CAGEset")`: aggregates TCs across all experiments into consensus clusters

clusterCTSS

  `signature(object = "CAGEset")`: clusters CTSSs into TCs per experiment

consensusClusters

  `signature(object = "CAGEset")`: extracts the genomic coordinates and other information on consensus clusters

consensusClustersTpm

  `signature(object = "CAGEset")`: extracts the matrix with tpm values for consensus clusters across all samples

cumulativeCTSSdistribution

  `signature(object = "CAGEset")`: calculates the cumulative distribution of CAGE signal along TCs or consensus clusters

exportCTSStoBedGraph

  `signature(object = "CAGEset")`: creates bedGraph files of CTSSs for visualization in the UCSC Genome Browser

exportToBed

  `signature(object = "CAGEset")`: creates various types of BED files for visualization in the UCSC Genome Browser

expressionClasses

  `signature(object = "CAGEset")`: extracts the labels of the expression classes of CTSSs or consensus clusters returned from expression profiling

extractExpressionClass

  `signature(object = "CAGEset")`: extracts CTSSs or consensus clusters belonging to specified expression class

genomeName

  `signature(object = "CAGEset")`: extracts the name of the BSgenome package used as the referent genome

getCTSS

  `signature(object = "CAGEset")`: reads in specified input files and fills in information on detected CTSSs and their tag count

getExpressionProfiles

  `signature(object = "CAGEset")`: performs expression clustering of CTSSs or consensus clusters across experiments

getShiftingPromoters

  `signature(object = "CAGEset")`: extracts consensus clusters with shifting score and/or FDR above specified threshold

inputFiles

  `signature(object = "CAGEset")`: extracts the paths of input CAGE data files

inputFilesType

  `signature(object = "CAGEset")`: extracts the type of input CAGE data files

librarySizes

  `signature(object = "CAGEset")`: extracts the library sizes of individual CAGE experiments within CAGEset object

mergeSamples

  `signature(object = "CAGEset", mergeIndex = "numeric")`: merges specified experiments (samples) into one (e.g. replicas)

normalizeTagCount

  `signature(object = "CAGEset")`: normalizes raw CAGE tag count

plotCorrelation

  `signature(object = "CAGEset")`: plots pairwise scatter plots and calculates correlation between samples

plotExpressionProfiles

  `signature(object = "CAGEset")`: creates file with beanplots of expression across experiments for CTSSs or consensus clusters belonging to different expression classes

plotInterquantileWidth

  `signature(object = "CAGEset")`: creates file with histograms of interquantile width

plotReverseCumulatives

  `signature(object = "CAGEset")`: creates file with reverse cumulative plots of CAGE tag count per CTSS

quantilePositions

  `signature(object = "CAGEset")`: calculates the positions of specified quantiles within TCs or consensus clusters

sampleLabels

  `signature(object = "CAGEset")`: extracts the labels of individual CAGE experiments within CAGEset object

scoreShift

  `signature(object = "CAGEset", groupX = "character", groupY = "character")`: calculates the shifting score and tests the statistical significance of differential TSS usage for consensus clusters between two specified (groups of) samples

setColors

  `signature(object = "CAGEset")`: assigns color to each sample to be used in visualisation

show

  `signature(object = "CAGEset")`: displays CAGEset object in a user friendly way

tagClusters

  `signature(object = "CAGEset")`: extracts the tag clusters for specified CAGE experiment

### Coercion

  `as(from, "CAGEset")`: Creates a CAGEset object from a data.frame object.

### Author(s)

Vanja Haberle

### Examples

    showClass("CAGEset")

[Package CAGEr version 1.30.3 Index]