aggregateTagClusters {CAGEr} | R Documentation

## Aggregate TCs across all samples

### Description

Aggregates tag clusters (TCs) across all CAGE datasets within the CAGEr object to create a referent set of consensus clusters.

### Usage

    aggregateTagClusters(object, tpmThreshold = 5,
      excludeSignalBelowThreshold = TRUE, qLow = NULL, qUp = NULL,
      maxDist = 100, useMulticore = FALSE, nrCores = NULL)

    ## S4 method for signature 'CAGEr'
    aggregateTagClusters(object, tpmThreshold = 5,
      excludeSignalBelowThreshold = TRUE, qLow = NULL, qUp = NULL,
      maxDist = 100, useMulticore = FALSE, nrCores = NULL)

### Arguments

`object` | A `CAGEr` object
`tpmThreshold` | Ignore tag clusters with normalized signal `< tpmThreshold` when constructing the consensus clusters.
`excludeSignalBelowThreshold` | When `TRUE` the tag clusters with normalized signal `< tpmThreshold` will not contribute to the total CAGE signal of a consensus cluster. When set to `FALSE` all TCs that overlap consensus clusters will contribute to the total signal, regardless whether they pass the threshold for constructing the clusters or not.
`qLow, qUp` | Set which "lower" (or "upper") quantile should be used as 5' (or 3') boundary of the tag cluster. If `NULL` the start (for `qLow`) or end (for `qUp`) position of the TC is used.
`maxDist` | Maximal length of the gap (in base-pairs) between two tag clusters for them to be part of the same consensus clusters.
`useMulticore` | Logical, should multicore be used (supported only on Unix-like platforms).
`nrCores` | Number of cores to use when `useMulticore = TRUE`. Default (`NULL`) uses all detected cores.

### Details

Since the tag clusters (TCs) returned by the `clusterCTSS` function are constructed separately for every CAGE sample within the CAGEr object, they can differ between samples in both their number, genomic coordinates, position of dominant TSS and #' overall signal. To be able to compare all samples at the level of clusters of TSSs, TCs from all CAGE datasets are aggregated into a single set of consensus clusters. First, TCs with signal `>= tpmThreshold` from all CAGE datasets are selected, and their 5' and 3' boundaries are determined based on provided `qLow` and `qUp` parameter (or the start and end coordinates, if they are set to `NULL`). Finally, the defined set of TCs from all CAGE datasets is reduced to a non-overlapping set of consensus clusters by merging overlapping TCs and TCs `<= maxDist` base-pairs apart. Consensus clusters represent a referent set of promoters that can be further used for expression profiling or detecting "shifting" (differentially used) promoters between different CAGE samples.

### Value

For `CAGEset` objects, the `consensusClusters` slot will be populated with a data frame indicating the cluster name, chromosome, start and end coordinates, the strand, and the normalised expression score of the cluster. This table is returned by the `consensusClusters` function.

For `CAGEexp` objects, the experiment `consensusClusters` will be occupied by a `RangedSummarizedExperiment` containing the cluster coodinates as row ranges, and their expression levels in the `counts` and `normalized` assays. These genomic ranges are returned by the `consensusClustersGR` function. The CTSS ranges of the `tagCountMatrix` experiment will gain a `cluster` column indicating which cluster they belong to. Lastly, the number of CTSS outside clusters will be documented in the `outOfClusters` column data. This table is returned by the `consensusClusters` function.

### Author(s)

Vanja Haberle

Charles Plessy

### See Also

Other CAGEr object modifiers: `CTSStoGenes`, `CustomConsensusClusters`, `annotateCTSS`, `clusterCTSS`, `cumulativeCTSSdistribution`, `getCTSS`, `normalizeTagCount`, `quantilePositions`, `summariseChrExpr`

Other CAGEr clusters functions: `CTSSclusteringMethod`, `CTSScumulativesTagClusters`, `CustomConsensusClusters`, `clusterCTSS`, `consensusClustersDESeq2`, `consensusClustersGR`, `cumulativeCTSSdistribution`, `plotInterquantileWidth`, `quantilePositions`, `tagClusters`

### Examples

    head(consensusClusters(exampleCAGEset))
    aggregateTagClusters( exampleCAGEset, tpmThreshold = 50
                        , excludeSignalBelowThreshold = FALSE, maxDist = 100)
    head(consensusClusters(exampleCAGEset))

    aggregateTagClusters(object = exampleCAGEset, tpmThreshold = 50,
      excludeSignalBelowThreshold = FALSE, qLow = 0.1, qUp = 0.9, maxDist = 100)
    head(consensusClusters(exampleCAGEset))

    consensusClustersGR(exampleCAGEexp)
    aggregateTagClusters( exampleCAGEexp, tpmThreshold = 50
                        , excludeSignalBelowThreshold = FALSE, maxDist = 100)
    consensusClustersGR(exampleCAGEexp)

    aggregateTagClusters( exampleCAGEexp, tpmThreshold = 50
                        , excludeSignalBelowThreshold = TRUE, maxDist = 100)
    consensusClustersGR(exampleCAGEexp)

    aggregateTagClusters( exampleCAGEexp, tpmThreshold = 50
                        , excludeSignalBelowThreshold = TRUE, maxDist = 100
                        , qLow = 0.1, qUp = 0.9)
    consensusClustersGR(exampleCAGEexp)

[Package CAGEr version 1.28.0 Index]