plotInterquantileWidth {CAGEr} | R Documentation

## Plot cluster widths

### Description

Plots histograms of the interquantile width of tag clusters or consensus clusters in each CAGE dataset.

### Usage

    plotInterquantileWidth(object, clusters = c("tagClusters",
      "consensusClusters"), tpmThreshold = 5, qLow = 0.1, qUp = 0.9,
      xlim = c(0, 150), ...)

    ## S4 method for signature 'CAGEr'
    plotInterquantileWidth(object,
      clusters = c("tagClusters", "consensusClusters"), tpmThreshold = 5,
      qLow = 0.1, qUp = 0.9, xlim = c(0, 150), ...)

### Arguments

`object` | A `CAGEr` object
`clusters` | Which clusters to be used. (`"tagClusters"` for tag clusters or `"consensusClusters"` for consensus clusters.
`tpmThreshold` | Exclude clusters with normalized signal `< tpmThreshold`.
`qLow, qUp` | Position of which "lower" (resp. "upper") quantile should be used as 5' (resp. 3') boundary. See Details.
`xlim` | The x axis limits of the plot.
`...` | Additional arguments passed to `plot()` function, such as `ylim`, etc..

### Details

Interquantile width is a width (in base-pairs) of the central part of the genomic region (bounded by the positions of specified `qLow` and `qUp` quantiles) that contains `>= (qUp - qLow) * 100%` of the CAGE signal. Positions of specified quantiles within each cluster have to be calculated beforehand by calling `quantilePositions` function. Interquantile width is a more robust measure of the promoter width than the total span of the region, because it takes into account the magnitude of the expression in the region.

### Author(s)

Vanja Haberle

### See Also

Other CAGEr plot functions: `hanabiPlot`, `plotAnnot`, `plotCorrelation`, `plotExpressionProfiles`, `plotReverseCumulatives`

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

### Examples

    plotInterquantileWidth( object = exampleCAGEset, clusters = "tagClusters"
                          , tpmThreshold = 50, qLow = 0.1, qUp = 0.9)

    plotInterquantileWidth( exampleCAGEexp, clusters = "consensusClusters"
                          , tpmThreshold = 50, qLow = 0.1, qUp = 0.9)

[Package CAGEr version 1.28.0 Index]