ExoDataBlacklist: ExoDataBlacklist

In welch16/ChIPexoQual: ChIPexoQual

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)

welch16/ChIPexoQual documentation built on May 4, 2019, 4:18 a.m.