ExoData-class {ChIPexoQual} | R Documentation

## ExoData object and constructors

### Description

`ExoData` is a subclass of `GenomicRanges`, used to asses the quality of ChIP-exo/nexus sample.

### Usage

    ExoData(file = NULL, reads = NULL, height = 1,
      mc.cores = getOption("mc.cores", 2L), save.reads = FALSE,
      nregions = 1000, ntimes = 100, verbose = TRUE)

### Arguments

`file` | a character value with location of the bam file with the aligned reads.
`reads` | a `GAlignments` object with the aligned reads of a ChIP-exo sample. It is meant to be used instead of `file`.
`height` | a numeric value indicating the value used to slice the coverage of the experiment into a set of regions.
`mc.cores` | a numeric value with the number of cores to use, i.e. at most how many child processes will be run simultaneously.
`save.reads` | a logical value to indicate if the reads are stored in the `ExoData` object. The default value is `FALSE`.
`nregions` | a numeric value indicating the number of regions sampled to estimate the quality parameter distributions. The default value is 1e3.
`ntimes` | a numeric value indicating the number of times that regions are sampled to estimate the quality parameter distributions. The default value is 1e2.
`verbose` | a logical value indicating if the user want to receive progress details. The default value is FALSE.

### Value

It returns an `ExoData` object with the regions obtained after partitioning the genome and the summary statistics for each region. If the `save.reads` parameter is `TRUE` then it contains a `GRanges` object with the reads of the ChIP-exo experiment.

### Examples

    files <- list.files(system.file("extdata",package = "ChIPexoQualExample"),
        full.names = TRUE)
    ExoData(files[5],mc.cores = 2L)

[Package ChIPexoQual version 1.11.0 Index]