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 2.11.4

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-- 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

-- 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
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.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