quantilePositions {CAGEr} | R Documentation

## Determine CTSS quantile positions within clusters

### Description

Calculates the positions of “upper” and “lower” quantiles of CAGE signal along tag clusters or consensus clusters in each sample of a CAGEr object.

### Usage

    quantilePositions(object, clusters = c("tagClusters",
      "consensusClusters"), qLow = 0.1, qUp = 0.9, useMulticore = FALSE,
      nrCores = NULL)

    ## S4 method for signature 'CAGEr'
    quantilePositions(object, clusters = c("tagClusters",
      "consensusClusters"), qLow = 0.1, qUp = 0.9, useMulticore = FALSE,
      nrCores = NULL)

### Arguments

`object` | A `CAGEr` object.
`clusters` | Either `tagClusters` or `consensusClusters`.
`qLow, qUp` | Which “lower” or “upper” quantiles should be calculated. Numeric vector of values in range `[0,1]`.
`useMulticore` | Logical, should multicore be used. `useMulticore = TRUE` has only effect on Unix-like platforms.
`nrCores` | Number of cores to use when `useMulticore = TRUE`. Default value `NULL` uses all detected cores.

### Details

From the 5' end the position, the position of a quantile q is detemined as the first base in which of the cumulative expression is higher or equal to q% of the total CAGE signal of that cluster. Promoter interquantile width is defined as the distance (in base pairs) between a “lower” and an “upper” quantile position.

### Value

When `clusters = "tagClusters"`, the slots `tagClustersQuantileLow` and `tagClustersQuantileUp` of a provided `CAGEset` object will be occupied with the positions of specified quantiles in all tag clusters for all CAGE datasets. When `clusters = "consensusClusters"` the slots `consensusClustersQuantileLow` and `consensusClustersQuantileUp` will be occupied by the corresponding information for consensus clusters.

In `CAGEexp` objects, the positions of the quantiles are defined reliatively to the start point of their cluster, for more efficient `Rle` compression. The quantile data for tag clusters are stored in the `TagClusters` objects directly. The quantile data for consensus clusters are stored in `integer` matrices named “q_x”, where x represents the quantile (for instance, `q_0.1`), and these matrices are assays of the `consensusClusters` `RangedSummarizedExperiment`.

### Author(s)

Vanja Haberle

### See Also

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

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

### Examples

    head(cbind(
      CAGEr:::tagClustersQuantileLow(exampleCAGEset, 1),
      CAGEr:::tagClustersQuantileUp (exampleCAGEset, 1)
    ))
    quantilePositions( object = exampleCAGEset, clusters = "tagClusters"
                     , qLow = c(0.1, 0.2), qUp = c(0.8, 0.9))
    head(cbind(
      CAGEr:::tagClustersQuantileLow(exampleCAGEset, 1),
      CAGEr:::tagClustersQuantileUp (exampleCAGEset,1 )
    ))

    cumulativeCTSSdistribution(exampleCAGEset, "consensusClusters") # Defaults in object do not fit
    quantilePositions( object = exampleCAGEset, clusters = "consensusClusters"
                     , qLow = c(0.1, 0.2), qUp = c(0.8, 0.9))

    head(cbind(
      CAGEr:::consensusClustersQuantileLow(exampleCAGEset, 1),
      CAGEr:::consensusClustersQuantileUp (exampleCAGEset , 1)
    ))

    quantilePositions(exampleCAGEexp, "tagClusters",       qLow = c(0.1, 0.2), qUp = c(0.8, 0.9))
    tagClustersGR(exampleCAGEexp)
    quantilePositions(exampleCAGEexp, "consensusClusters", qLow = c(0.1, 0.2), qUp = c(0.8, 0.9))

[Package CAGEr version 1.34.0 Index]