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

## Documentation for package ‘CAGEr’ version 1.24.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N P Q R S T misc

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

## -- A --

aggregateTagClusters | Aggregate TCs across all samples
aggregateTagClusters-method | Aggregate TCs across all samples
annotateConsensusClusters | Annotate and compute summary statistics
annotateConsensusClusters-method | Annotate and compute summary statistics
annotateCTSS | Annotate and compute summary statistics
annotateCTSS-method | Annotate and compute summary statistics

## -- B --

bam2CTSS | bam2CTSS

## -- C --

CAGEexp | CAGEr class to hold all data and metadata about one CAGE experiment.
CAGEexp-class | CAGEr class to hold all data and metadata about one CAGE experiment.
CAGEr | CAGEr objects
CAGEr-class | CAGEr objects
CAGEr_Multicore | Multicore support in CAGEr
CAGEset | Class '"CAGEset"'
CAGEset-class | Class '"CAGEset"'
CCdataframe2granges | Private functions to convert CC formats
CCgranges2dataframe | Private functions to convert CC formats
clusterCTSS | Cluster CTSSs into tag clusters
clusterCTSS-method | Cluster CTSSs into tag clusters
coerce-method | CAGEr class to hold all data and metadata about one CAGE experiment.
coerce-method | Class '"CAGEset"'
coerceInBSgenome | coerceInBSgenome
consensusClusterConvertors | Private functions to convert CC formats
ConsensusClusters | Classes for type safety.
consensusClusters | Get consensus clusters from CAGEr objects
consensusClusters-method | Get consensus clusters from CAGEr objects
consensusClusters<- | Set consensus clusters from CAGEr objects
consensusClusters<--method | Set consensus clusters from CAGEr objects
consensusClustersDESeq2 | Export _consensus cluster_ expression data for DESeq2 analysis
consensusClustersDESeq2-method | Export _consensus cluster_ expression data for DESeq2 analysis
consensusClustersGR | Get consensus clusters from CAGEr objects
consensusClustersGR-method | Get consensus clusters from CAGEr objects
consensusClustersGR<- | Set consensus clusters from CAGEr objects
consensusClustersGR<--method | Set consensus clusters from CAGEr objects
consensusClustersQuantile | Quantile metadata stored in CAGEr objects.
consensusClustersQuantile-method | Quantile metadata stored in CAGEr objects.
consensusClustersQuantileLow | Quantile metadata stored in CAGEr objects.
consensusClustersQuantileLow-method | Quantile metadata stored in CAGEr objects.
consensusClustersQuantileLow<- | Quantile metadata stored in CAGEr objects.
consensusClustersQuantileLow<--method | Quantile metadata stored in CAGEr objects.
consensusClustersQuantileUp | Quantile metadata stored in CAGEr objects.
consensusClustersQuantileUp-method | Quantile metadata stored in CAGEr objects.
consensusClustersQuantileUp<- | Quantile metadata stored in CAGEr objects.
consensusClustersQuantileUp<--method | Quantile metadata stored in CAGEr objects.
consensusClustersSE | Get consensus clusters from CAGEr objects
consensusClustersSE-method | Get consensus clusters from CAGEr objects
consensusClustersSE<- | Set consensus clusters from CAGEr objects
consensusClustersSE<--method | Set consensus clusters from CAGEr objects
consensusClustersTpm | Extracting consensus clusters tpm matrix from CAGEset object
consensusClustersTpm-method | Extracting consensus clusters tpm matrix from CAGEset object
coverage-functions | Private functions behind 'cumulativeCTSSdistribution'
CTSS | Classes for type safety.
CTSS-class | Classes for type safety.
CTSS.chr | Classes for type safety.
CTSS.chr-class | Classes for type safety.
CTSSclusteringMethod | Get /set CTSS clustering method
CTSSclusteringMethod-method | Get /set CTSS clustering method
CTSSclusteringMethod<- | Get /set CTSS clustering method
CTSSclusteringMethod<--method | Get /set CTSS clustering method
CTSScoordinates | Genomic coordinates of TSSs from a 'CAGEr' object
CTSScoordinates-method | Genomic coordinates of TSSs from a 'CAGEr' object
CTSScoordinatesGR | Genomic coordinates of TSSs from a 'CAGEr' object
CTSScoordinatesGR-method | Genomic coordinates of TSSs from a 'CAGEr' object
CTSScoordinatesGR<- | Genomic coordinates of TSSs from a 'CAGEr' object
CTSScoordinatesGR<--method | Genomic coordinates of TSSs from a 'CAGEr' object
CTSScumulativesCC | Get/set CTSS cumulative TC or CC data
CTSScumulativesCC-method | Get/set CTSS cumulative TC or CC data
CTSScumulativesTagClusters | Get/set CTSS cumulative TC or CC data
CTSScumulativesTagClusters-method | Get/set CTSS cumulative TC or CC data
CTSScumulativesTagClusters<- | Get/set CTSS cumulative TC or CC data
CTSScumulativesTagClusters<--method | Get/set CTSS cumulative TC or CC data
CTSSnormalizedTpm | Extracting normalized CAGE signal for TSSs from CAGEr objects
CTSSnormalizedTpm-method | Extracting normalized CAGE signal for TSSs from CAGEr objects
CTSSnormalizedTpmDF | Extracting normalized CAGE signal for TSSs from CAGEr objects
CTSSnormalizedTpmDf | Extracting normalized CAGE signal for TSSs from CAGEr objects
CTSSnormalizedTpmDF-method | Extracting normalized CAGE signal for TSSs from CAGEr objects
CTSSnormalizedTpmDf-method | Extracting normalized CAGE signal for TSSs from CAGEr objects
CTSSnormalizedTpmGR | Extracting normalized CAGE signal for TSSs from CAGEr objects
CTSSnormalizedTpmGR-method | Extracting normalized CAGE signal for TSSs from CAGEr objects
CTSStagCount | Extract raw CAGE TSSs expression tables from 'CAGEr' objects
CTSStagCount-method | Extract raw CAGE TSSs expression tables from 'CAGEr' objects
CTSStagCountDA | Extract raw CAGE TSSs expression tables from 'CAGEr' objects
CTSStagCountDA-method | Extract raw CAGE TSSs expression tables from 'CAGEr' objects
CTSStagCountDF | Extract raw CAGE TSSs expression tables from 'CAGEr' objects
CTSStagCountDf | Extract raw CAGE TSSs expression tables from 'CAGEr' objects
CTSStagCountDF-method | Extract raw CAGE TSSs expression tables from 'CAGEr' objects
CTSStagCountDf-method | Extract raw CAGE TSSs expression tables from 'CAGEr' objects
CTSStagCountGR | Extract raw CAGE TSSs expression tables from 'CAGEr' objects
CTSStagCountGR-method | Extract raw CAGE TSSs expression tables from 'CAGEr' objects
CTSStagCountSE | Extract raw CAGE TSSs expression tables from 'CAGEr' objects
CTSStagCountSE-method | Extracting CAGE tag count for TSSs from CAGEr objects
CTSStagCountSE<- | Genomic coordinates of TSSs from a 'CAGEr' object
CTSStagCountSE<--method | Genomic coordinates of TSSs from a 'CAGEr' object
CTSStagCountTable | Extracting CAGE tag count for TSSs from CAGEr objects
CTSStagCountTable-method | Extracting CAGE tag count for TSSs from CAGEr objects
CTSStoGenes | Make a gene expression table.
CTSStoGenes-method | Make a gene expression table.
cumulativeCTSSdistribution | Cumulative sums of CAGE counts along genomic regions
cumulativeCTSSdistribution-method | Cumulative sums of CAGE counts along genomic regions
CustomConsensusClusters | Expression levels of consensus cluster
CustomConsensusClusters-method | Expression levels of consensus cluster

## -- D --

distclu-functions | Private functions for distance clustering.

## -- E --

exampleCAGEexp | Example CAGEexp object.
exampleCAGEset | Example CAGEset object with zebrafish CAGE data
exampleZv9_annot | Example zebrafish annotation data
exportCTSStoBedGraph | Creating bedGraph/bigWig tracks of CAGE transcription starts sites
exportCTSStoBedGraph-method | Creating bedGraph/bigWig tracks of CAGE transcription starts sites
exportToBed | Create BED tracks of TSSs and clusters of TSSs
exportToBed-method | Create BED tracks of TSSs and clusters of TSSs
expressionClasses | Extract labels of expression classes
expressionClasses-method | Extract labels of expression classes
extractExpressionClass | Extract elements of the specified expression class
extractExpressionClass-method | Extract elements of the specified expression class

## -- F --

FANTOM5humanSamples | List of FANTOM5 human CAGE samples
FANTOM5mouseSamples | List of FANTOM5 mouse CAGE samples
findStrandInvaders | Detect and remove strand invasion artefacts
findStrandInvaders-method | Detect and remove strand invasion artefacts

## -- G --

GeneExpDESeq2 | Export gene expression data for DESeq2 analysis
GeneExpDESeq2-method | Export gene expression data for DESeq2 analysis
GeneExpSE | Retreives the SummarizedExperiment containing gene expression levels.
GeneExpSE-method | Retreives the SummarizedExperiment containing gene expression levels.
genomeName | Extracting genome name from CAGEr objects
genomeName-method | Extracting genome name from CAGEr objects
genomeName<- | Extracting genome name from CAGEr objects
genomeName<--method | Extracting genome name from CAGEr objects
getCTSS | Reading CAGE data from input file(s) and detecting TSSs
getCTSS-method | Reading CAGE data from input file(s) and detecting TSSs
getExpressionProfiles | CAGE data based expression clustering
getExpressionProfiles-method | CAGE data based expression clustering
getShiftingPromoters | Select consensus clusters with shifting score above threshold
getShiftingPromoters-method | Select consensus clusters with shifting score above threshold

## -- H --

hanabi | Calcultate richness in preparation for plotting
hanabi-class | Hanabi class
hanabi-method | Calcultate richness in preparation for plotting
hanabiPlot | hanabiPlot

## -- I --

import.bam | import.bam
import.bam.ctss | import.bam.ctss
import.bedCTSS | import.bedCTSS
import.bedmolecule | import.bedmolecule
import.bedScore | import.bedScore
import.CAGEscanMolecule | import.CAGEscanMolecule
import.CTSS | import.CTSS
importPublicData | Importing publicly available CAGE data from various resources
importPublicData-method | Importing publicly available CAGE data from various resources
inputFiles | Extracting paths to input files from CAGEr objects
inputFiles-method | Extracting paths to input files from CAGEr objects
inputFiles<- | Extracting paths to input files from CAGEr objects
inputFiles<--method | Extracting paths to input files from CAGEr objects
inputFilesType | Input file formats for CAGEr objects
inputFilesType-method | Input file formats for CAGEr objects
inputFilesType<- | Input file formats for CAGEr objects
inputFilesType<--method | Input file formats for CAGEr objects

## -- L --

librarySizes | Extracting library sizes from CAGEr objects
librarySizes-method | Extracting library sizes from CAGEr objects
lines.hanabi | Plotting Hanabi objects
loadFileIntoGPos | loadFileIntoGPos

## -- M --

mapStats | Process mapping statistics
mapStatsScopes | mapStats scopes
mergeCAGEsets | Merge two CAGEr objects into one
mergeCAGEsets-method | Merge two CAGEr objects into one
mergeSamples | Merge CAGE samples
mergeSamples-method | Merge CAGE samples
moleculesGR2CTSS | moleculesGR2CTSS
msScope_all | mapStats scopes
msScope_annotation | mapStats scopes
msScope_counts | mapStats scopes
msScope_mapped | mapStats scopes
msScope_qc | mapStats scopes
msScope_steps | mapStats scopes

## -- N --

normalizeTagCount | Normalizing raw CAGE tag count
normalizeTagCount-method | Normalizing raw CAGE tag count

## -- P --

parseCAGEscanBlocksToGrangeTSS | parseCAGEscanBlocksToGrangeTSS
plot.hanabi | Plotting Hanabi objects
plotAnnot | Plot annotation statistics
plotAnnot-method | Plot annotation statistics
plotCorrelation | Pairwise scatter plots and correlations of CAGE signal
plotCorrelation-method | Pairwise scatter plots and correlations of CAGE signal
plotCorrelation2 | Pairwise scatter plots and correlations of CAGE signal
plotCorrelation2-method | Pairwise scatter plots and correlations of CAGE signal
plotExpressionProfiles | Plotting expression profiles derived from CAGE data
plotExpressionProfiles-method | Plotting expression profiles derived from CAGE data
plotInterquantileWidth | Plot cluster widths
plotInterquantileWidth-method | Plot cluster widths
plotReverseCumulatives | Plot reverse cumulative number of CAGE tags per CTSS
plotReverseCumulatives-method | Plot reverse cumulative number of CAGE tags per CTSS
points.hanabi | Plotting Hanabi objects

## -- Q --

quantilePositions | Determine CTSS quantile positions within clusters
quantilePositions-method | Determine CTSS quantile positions within clusters

## -- R --

ranges2annot | Hierarchical annotation of CTSSes
ranges2genes | ranges2genes
ranges2names | ranges2names
removeStrandInvaders | Detect and remove strand invasion artefacts
removeStrandInvaders-method | Detect and remove strand invasion artefacts

## -- S --

sampleLabels | Get and set sample labels
sampleLabels-method | Get and set sample labels
sampleLabels<- | Get and set sample labels
sampleLabels<--method | Get and set sample labels
sampleList | Get and set sample labels
sampleList-method | Get and set sample labels
scoreShift | Calculate promoter shifting score
scoreShift-method | Calculate promoter shifting score
seqNameTotalsSE | Retreives the SummarizedExperiment containing chromosome expression totals.
seqNameTotalsSE-method | Retreives the SummarizedExperiment containing chromosome expression totals.
seqNameTotalsSE<- | Retreives the SummarizedExperiment containing chromosome expression totals.
setColors | Set colors for samples
setColors-method | Set colors for samples
show-method | Methods for function 'show'
show-methods | Methods for function 'show'
Strand invaders | Detect and remove strand invasion artefacts
summariseChrExpr | Expression levels by chromosomes
summariseChrExpr-method | Expression levels by chromosomes

## -- T --

tagClusterConvertors | Private functions to convert TC formats
TagClusters | Classes for type safety.
tagClusters | Extract tag clusters (TCs) for individual CAGE experiments
tagClusters-method | Extract tag clusters (TCs) for individual CAGE experiments
tagClustersGR | Extract tag clusters (TCs) for individual CAGE experiments
tagClustersGR-method | Extract tag clusters (TCs) for individual CAGE experiments
tagClustersGR<- | Extract tag clusters (TCs) for individual CAGE experiments
tagClustersGR<--method | Extract tag clusters (TCs) for individual CAGE experiments
tagClustersQuantile | Quantile metadata stored in CAGEr objects.
tagClustersQuantile-method | Quantile metadata stored in CAGEr objects.
tagClustersQuantileLow | Quantile metadata stored in CAGEr objects.
tagClustersQuantileLow-method | Quantile metadata stored in CAGEr objects.
tagClustersQuantileLow<- | Quantile metadata stored in CAGEr objects.
tagClustersQuantileLow<--method | Quantile metadata stored in CAGEr objects.
tagClustersQuantileUp | Quantile metadata stored in CAGEr objects.
tagClustersQuantileUp-method | Quantile metadata stored in CAGEr objects.
tagClustersQuantileUp<- | Quantile metadata stored in CAGEr objects.
tagClustersQuantileUp<--method | Quantile metadata stored in CAGEr objects.
TCdataframe2granges | Private functions to convert TC formats
TCgranges2dataframe | Private functions to convert TC formats

## -- misc --

.byCtss | Apply functions to identical CTSSes.
.byCtss-method | Apply functions to identical CTSSes.
.cluster.ctss.chr | Private functions for distance clustering.
.cluster.ctss.strand | Private functions for distance clustering.
.clusterAggregateAndSum | Aggregate identical clusters and sum their scores.
.clusterAggregateAndSum-method | Aggregate identical clusters and sum their scores.
.ConsensusClusters | Classes for type safety.
.CTSS | Classes for type safety.
.CTSS.chr | Classes for type safety.
.ctss2clusters | Private functions for distance clustering.
.distclu | Private functions for distance clustering.
.get.quant.pos | Get quantile positions
.getCAGEsignalCoverage | Private functions behind 'cumulativeCTSSdistribution'
.getCumsum | Private functions behind 'cumulativeCTSSdistribution'
.getCumsumChr2 | Private functions behind 'cumulativeCTSSdistribution'
.hanabi | Hanabi class
.powerLaw | .powerLaw
.summarize.clusters | Private functions for distance clustering.
.TagClusters | Classes for type safety.