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 1.18.1

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CAGEr-package Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
aggregateTagClusters Aggregating tag clusters across multiple CAGE datasets
aggregateTagClusters-method Aggregating tag clusters across multiple CAGE datasets
CAGEr Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
CAGEset Class '"CAGEset"'
CAGEset-class Class '"CAGEset"'
clusterCTSS Clustering CTSSs into tag clusters (TCs)
clusterCTSS-method Clustering CTSSs into tag clusters (TCs)
coerce-method Class '"CAGEset"'
consensusClusters Extracting consensus clusters from CAGEset object
consensusClusters-method Extracting consensus clusters from CAGEset object
consensusClustersTpm Extracting consensus clusters tpm matrix from CAGEset object
consensusClustersTpm-method Extracting consensus clusters tpm matrix from CAGEset object
CTSSclusteringMethod Extracting CTSS clustering method from CAGEset object
CTSSclusteringMethod-method Extracting CTSS clustering method from CAGEset object
CTSScoordinates Extracting genomic coordinates of TSSs from CAGEset object
CTSScoordinates-method Extracting genomic coordinates of TSSs from CAGEset object
CTSSnormalizedTpm Extracting normalized CAGE signal for TSSs from CAGEset object
CTSSnormalizedTpm-method Extracting normalized CAGE signal for TSSs from CAGEset object
CTSStagCount Extracting CAGE tag count for TSSs from CAGEset object
CTSStagCount-method Extracting CAGE tag count for TSSs from CAGEset object
cumulativeCTSSdistribution Calculating cumulative sum of CAGE signal along genomic region
cumulativeCTSSdistribution-method Calculating cumulative sum of CAGE signal along genomic region
exampleCAGEset Example CAGEset object with zebrafish CAGE data
exportCTSStoBedGraph Creating bedGraph/bigWig tracks of CAGE transcription starts sites
exportCTSStoBedGraph-method Creating bedGraph/bigWig tracks of CAGE transcription starts sites
exportToBed Creating BED tracks of TSSs and clusters of TSSs
exportToBed-method Creating BED tracks of TSSs and clusters of TSSs
expressionClasses Extracting labels of expression classes
expressionClasses-method Extracting labels of expression classes
extractExpressionClass Extracting elements of the specified expression class
extractExpressionClass-method Extracting elements of the specified expression class
FANTOM5humanSamples List of FANTOM5 human CAGE samples
FANTOM5mouseSamples List of FANTOM5 mouse CAGE samples
genomeName Extracting genome name from CAGEset object
genomeName-method Extracting genome name from CAGEset object
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 Selecting consensus clusters with shifting score above specified threshold
getShiftingPromoters-method Selecting consensus clusters with shifting score above specified threshold
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 CAGEset object
inputFiles-method Extracting paths to input files from CAGEset object
inputFilesType Extracting type of input files from CAGEset object
inputFilesType-method Extracting type of input files from CAGEset object
librarySizes Extracting library sizes from CAGEset object
librarySizes-method Extracting library sizes from CAGEset object
mergeCAGEsets Merging two CAGEset objects into one
mergeCAGEsets-method Merging two CAGEset objects into one
mergeSamples Merging CAGE datasets (samples)
mergeSamples-method Merging CAGE datasets (samples)
normalizeTagCount Normalizing raw CAGE tag count
normalizeTagCount-method Normalizing raw CAGE tag count
plotCorrelation Plotting pairwise scatter plots of CAGE signal and calculating correlation between samples
plotCorrelation-method Plotting pairwise scatter plots of CAGE signal and calculating correlation between samples
plotExpressionProfiles Plotting expression profiles derived from CAGE data
plotExpressionProfiles-method Plotting expression profiles derived from CAGE data
plotInterquantileWidth Plotting distribution of interquantile width
plotInterquantileWidth-method Plotting distribution of interquantile width
plotReverseCumulatives Plotting reverse cumulative number of CAGE tags per CTSS
plotReverseCumulatives-method Plotting reverse cumulative number of CAGE tags per CTSS
quantilePositions Determining positions of CAGE signal quantiles within genomic region
quantilePositions-method Determining positions of CAGE signal quantiles within genomic region
sampleLabels Extracting CAGE datasets labels from CAGEset object
sampleLabels-method Extracting CAGE datasets labels from CAGEset object
scoreShift Calculating promoter shifting score
scoreShift-method Calculating promoter shifting score
setColors Setting colors for samples
setColors-method Setting colors for samples
show-method Methods for function 'show'
show-methods Methods for function 'show'
tagClusters Extracting tag clusters (TCs) for individual CAGE experiment from CAGEset object
tagClusters-method Extracting tag clusters (TCs) for individual CAGE experiment from CAGEset object