ExoDataBlacklist {ChIPexoQual} | R Documentation

## ExoDataBlacklist

### Description

`ExoDataBlacklist` separates the regions in an `ExoData` object by overlapping them with a set of blacklisted regions and calculates the quality parameters in both collections of islands.

### Usage

    ExoDataBlacklist(exo, blacklist, which.param = "beta1", nregions = NULL,
      ntimes = NULL)

### Arguments

`exo` | a `ExoData` object.
`blacklist` | a `GRanges` object with the blacklisted regions or a `character` indicating which of the blacklist included in `ChIPexoQual` to use.
`which.param` | a character value with either `"beta1"` or `"beta2"` that determines which parameters in the model depth_i ~ uniquePos_i + width_i to plot. The default value is `"beta1"`.
`nregions` | a numeric value indicating the number of regions sampled to estimate the quality parameter distributions. The default value is extracted from `exo`.
`ntimes` | a numeric value indicating the number of times that regions are sampled to estimate the quality parameter distributions. The default value is extracted from `object`.

### Value

A `ggplot` object with a boxplot that compares the quality scores distribution when the regions overlap a pre-defined collection of blacklists.

### Examples

    data(exoExample)
    data(blacklists)
    ExoDataBlacklist(exoExample,blacklists[["mm9"]],ntimes = 10,nregions = 500)

[Package ChIPexoQual version 1.4.0 Index]