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

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Documentation for package ‘CAGEr’ version 2.8.0

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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
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 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
coverage-functions Private functions behind 'cumulativeCTSSdistribution'
CTSS CAGE Transcription Start Sites
CTSS-class CAGE Transcription Start Sites
CTSS.chr-class CAGE Transcription Start Sites
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
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
CTSStagCountDA Raw CAGE TSSs expression counts
CTSStagCountDA-method Raw CAGE TSSs expression counts
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-functions Private functions for 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
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

-- 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
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 --

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

-- 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.
.ConsensusClusters ConsensusClusters
.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 TagClusters