ExoDataSubsampling {ChIPexoQual} | R Documentation

## ExoDataSubsampling

### Description

`ExoDataSubsampling` samples `sample.reads` from the ChIP-exo experiment and creates a list of `ExoData` objects

### Usage

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

### 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`.
`sample.depth` | a numeric vector with the number of reads to be sampled.
`height` | a numeric value indicating the value used to slice the coverage of the experiment into a set of regions.
`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.
`save.reads` | a logical value to indicate if the reads are stored in the `ExoData` object. The default value is `FALSE`.
`mc.cores` | a numeric value with the number of cores to use, i.e. at most how many child processes will be run simultaneously.

### 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)
    sample.depth <- seq(1e5,2e5,5e4)
    ExoDataSubsampling(file = files[5],sample.depth = sample.depth)

[Package ChIPexoQual version 1.4.0 Index]