Man pages for CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
| aggregateTagClusters | Aggregate TCs across all samples |
| annotateCTSS | Annotate and compute summary statistics |
| bam2CTSS | bam2CTSS |
| byCtss | Apply functions to identical CTSSes. |
| CAGEexp-class | CAGEr class to hold all data and metadata about one CAGE... |
| CAGEr-class | CAGEr objects |
| CAGEr_Multicore | Multicore support in CAGEr |
| CAGEr-package | Analysis of CAGE (Cap Analysis of Gene Expression) sequencing... |
| CAGEset-class | Class '"CAGEset"' |
| clusterAggregateAndSum | Aggregate identical clusters and sum their scores. |
| clusterCTSS | Cluster CTSSs into tag clusters |
| coerceInBSgenome | coerceInBSgenome |
| consensusClusterConvertors | Private functions to convert CC formats |
| consensusClusters | Get consensus clusters from CAGEr objects |
| consensusClustersDESeq2 | Export _consensus cluster_ expression data for DESeq2... |
| consensusClustersQuantile | Quantile metadata stored in CAGEr objects. |
| consensusClusters-set | Set consensus clusters from CAGEr objects |
| consensusClustersTpm | Extracting consensus clusters tpm matrix from CAGEset object |
| coverage-functions | Private functions behind 'cumulativeCTSSdistribution' |
| CTSS-class | CAGE Transcription Start Sites |
| CTSSclusteringMethod | Get /set CTSS clustering method |
| CTSScoordinates | Genomic coordinates of TSSs from a 'CAGEr' object |
| CTSScumulativesTagClusters | Get/set CTSS cumulative TC or CC data |
| CTSSnormalizedTpm | Extracting normalized CAGE signal for TSSs from CAGEr objects |
| CTSStagCount | Extract raw CAGE TSSs expression tables from 'CAGEr' objects |
| CTSStagCountTable | Extracting CAGE tag count for TSSs from CAGEr objects |
| CTSStoGenes | Make a gene expression table. |
| cumulativeCTSSdistribution | Cumulative sums of CAGE counts along genomic regions |
| CustomConsensusClusters | Expression levels of consensus cluster |
| distclu-functions | Private functions for distance clustering. |
| 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... |
| exportToBed | Create BED tracks of TSSs and clusters of TSSs |
| expressionClasses | Extract labels of expression classes |
| extractExpressionClass | Extract elements of the specified expression class |
| FANTOM5humanSamples | List of FANTOM5 human CAGE samples |
| FANTOM5mouseSamples | List of FANTOM5 mouse CAGE samples |
| GeneExpDESeq2 | Export gene expression data for DESeq2 analysis |
| GeneExpSE | Retreives the SummarizedExperiment containing gene expression... |
| genomeName | Extracting genome name from CAGEr objects |
| getCTSS | Reading CAGE data from input file(s) and detecting TSSs |
| getExpressionProfiles | CAGE data based expression clustering |
| getShiftingPromoters | Select consensus clusters with shifting score above threshold |
| hanabi | Calcultate richness in preparation for plotting |
| hanabi-class | Hanabi class |
| hanabiPlot | hanabiPlot |
| 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 |
| inputFiles | Extracting paths to input files from CAGEr objects |
| inputFilesType | Input file formats for CAGEr objects |
| librarySizes | Extracting library sizes from CAGEr objects |
| loadFileIntoGPos | loadFileIntoGPos |
| mapStats | Process mapping statistics |
| mapStatsScopes | mapStats scopes |
| mergeCAGEsets | Merge two CAGEr objects into one |
| mergeSamples | Merge CAGE samples |
| moleculesGR2CTSS | moleculesGR2CTSS |
| normalizeTagCount | Normalizing raw CAGE tag count |
| parseCAGEscanBlocksToGrangeTSS | parseCAGEscanBlocksToGrangeTSS |
| plotAnnot | Plot annotation statistics |
| plotCorrelation | Pairwise scatter plots and correlations of CAGE signal |
| plotExpressionProfiles | Plotting expression profiles derived from CAGE data |
| plot.hanabi | Plotting Hanabi objects |
| plotInterquantileWidth | Plot cluster widths |
| plotReverseCumulatives | Plot reverse cumulative number of CAGE tags per CTSS |
| powerLaw | .powerLaw |
| quantilePositions | Determine CTSS quantile positions within clusters |
| QuantileWidthFunctions | Get quantile positions |
| ranges2annot | Hierarchical annotation of CTSSes |
| ranges2genes | ranges2genes |
| ranges2names | ranges2names |
| sampleLabels | Get and set sample labels |
| scoreShift | Calculate promoter shifting score |
| seqNameTotalsSE | Retreives the SummarizedExperiment containing chromosome... |
| setColors | Set colors for samples |
| show-methods | Methods for function 'show' |
| strandInvaders | Detect and remove strand invasion artefacts |
| summariseChrExpr | Expression levels by chromosomes |
| tagClusterConvertors | Private functions to convert TC formats |
| tagClusters | Extract tag clusters (TCs) for individual CAGE experiments |
| tagClustersQuantile | Quantile metadata stored in CAGEr objects. |
