# 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 2.16.0

- 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

## -- 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
annotateTagClusters | Annotate and compute summary statistics
annotateTagClusters-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-class | CAGEr objects
CAGEr_Multicore | Multicore support in CAGEr
coerce-method | CAGEr class to hold all data and metadata about one CAGE experiment.
coerce-method | CAGE Transcription Start Sites
coerceInBSgenome | coerceInBSgenome
ConsensusClusters | ConsensusClusters
ConsensusClusters-class | ConsensusClusters
consensusClusters<- | 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.
consensusClustersQuantileUp | Quantile metadata stored in CAGEr objects.
consensusClustersQuantileUp-method | Quantile metadata stored in CAGEr objects.
consensusClustersQuantileUp<- | 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 CAGEr object
consensusClustersTpm-method | Extracting consensus clusters tpm matrix from CAGEr object
correlationMatrix | Pairwise scatter plots and correlations of CAGE signal
correlationMatrix-method | Pairwise scatter plots and correlations of CAGE signal
CTSS | CAGE Transcription Start Sites
CTSS-class | CAGE Transcription Start Sites
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
CTSSnormalizedTpmDF | 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
CTSStagCountDF | Raw CAGE TSSs expression counts
CTSStagCountDF-method | Raw CAGE TSSs expression counts
CTSStagCountGR | Raw CAGE TSSs expression counts
CTSStagCountGR-method | Raw CAGE TSSs expression counts
CTSStagCountSE | Raw CAGE TSSs expression counts
CTSStagCountSE-method | Raw CAGE TSSs expression counts
CTSStagCountSE<- | Genomic coordinates of TSSs from a 'CAGEr' object
CTSStagCountSE<--method | Genomic coordinates of TSSs from a 'CAGEr' object
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 | Distance clustering
distclu-method | Distance clustering

## -- E --

exampleCAGEexp | Example CAGEexp object.
exampleZv9_annot | Example zebrafish annotation data
exportToTrack | Converts TSSs and clusters of TSSs to a genome browser track format
exportToTrack-method | Converts TSSs and clusters of TSSs to a genome browser track format
expressionClasses | Extract labels of _expression classes_
expressionClasses-method | Extract labels of _expression classes_

## -- F --

FANTOM5humanSamples | FANTOM5 human samples
FANTOM5mouseSamples | FANTOM5 mouse samples
filteredCTSSidx | The 'filteredCTSSidx()' function is in _CAGEr_ functions to retrieve the result of the 'flagLowExpCTSS()' function in a safe way.
filteredCTSSidx-method | The 'filteredCTSSidx()' function is in _CAGEr_ functions to retrieve the result of the 'flagLowExpCTSS()' function in a safe way.
filterLowExpCTSS | Flag CTSSes based on sample expression
filterLowExpCTSS-method | Flag CTSSes based on sample expression
findStrandInvaders | Detect and remove strand invasion artefacts
findStrandInvaders-method | Detect and remove strand invasion artefacts
flagByUpstreamSequences | Filter by upstream sequences
flagByUpstreamSequences-method | Filter by upstream sequences
flagLowExpCTSS | Flag CTSSes based on sample expression
flagLowExpCTSS-method | Flag CTSSes based on sample expression

## -- 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.bigwig | Read in BigWig files to CAGEexp object
import.CAGEscanMolecule | import.CAGEscanMolecule
import.CTSS | import.CTSS
importPublicData | importPublicData
importPublicData-method | importPublicData
initialize-method | CAGE Transcription Start Sites
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 --

paraclu | Parametric clustering
paraclu-method | Parametric clustering
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 | Plot CAGE expression profiles
plotExpressionProfiles-method | Plot CAGE expression profiles
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
quickEnhancers | Identify and quantify enhancers.
quickEnhancers-method | Identify and quantify enhancers.

## -- R --

ranges2annot | Hierarchical annotation of genomic regions.
ranges2genes | ranges2genes
ranges2names | ranges2names
removeStrandInvaders | Detect and remove strand invasion artefacts
removeStrandInvaders-method | Detect and remove strand invasion artefacts
resetCAGEexp | Reset a CAGEexp object
resetCAGEexp-method | Reset a CAGEexp object
rowsum.RleDataFrame | rowsum function for Rle DataFrames
rowSums.RleDataFrame | rowSums function for Rle DataFrames

## -- 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 | CAGE Transcription Start Sites
Strand invaders | Detect and remove strand invasion artefacts
summariseChrExpr | Expression levels by chromosomes
summariseChrExpr-method | Expression levels by chromosomes

## -- T --

TagClusters | TagClusters
TagClusters-class | TagClusters
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
TSSlogo | TSS logo
TSSlogo-method | TSS logo

## -- misc --

.byCtss | Apply functions to identical CTSSes.
.byCtss-method | Apply functions to identical CTSSes.
.ConsensusClusters | ConsensusClusters
.ctss_summary_for_clusters | Summarise CTSSs included in clusters
.get.quant.pos | Get quantile positions
.hanabi | Hanabi class
.powerLaw | .powerLaw
.TagClusters | TagClusters