CAGEset-class: Class '"CAGEset"'

In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

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")

CAGEr documentation built on Jan. 17, 2021, 2 a.m.