segReads-class {PICS} | R Documentation

## Classes and functions to segment the genome in candidate regions

### Description

Pre-process bidirectional aligned reads data from a single ChIP-Seq experiment to detect candidate regions with a minimum number of forward and reverse reads. These candidate regions will then be processed by `PICS`.

### Usage

    segReads(yF, yR, cF, cR, map, chr)

    segReadsList(List, paraSW, N, Nc)

    ## S4 method for signature 'segReads'
    show(object)

    ## S4 method for signature 'segReadsList'
    show(object)

    map(x, ...)

    ## S4 method for signature 'segReads'
    map(x)

    ## S4 method for signature 'segReadsList'
    map(x)

    ## S4 method for signature 'segReadsList'
    length(x)

    ## S4 method for signature 'segReadsList'
    summary(object)

    ## S4 method for signature 'segReads'
    summary(object)

    ## S4 method for signature 'segReadsList,ANY,ANY,ANY'
    x[i, j, ..., drop = FALSE]

    ## S4 method for signature 'segReadsList,ANY,ANY'
    x[[i, j, ..., exact = TRUE]]

### Arguments

`yF` | A `numeric` vector. Forward reads.
`yR` | A `numeric` vector. Reverse reads.
`cF` | A `numeric` vector. Forward reads for the controls.
`cR` | A `numeric` vector. Reverse reads for the controls.
`map` | A `matrix`. The mappability profile.
`chr` | A `character`. Chromosome name.
`List` | A `list` of `segReads` objects.
`paraSW` | A `list` of parameters for the genomic regions.
`N` | A `numeric`. The number of reads in the data.
`Nc` | A `numeric`. The number of reads in the control.
`object, x` | A `segReads` object.
`i, j, ..., exact, drop` | Additional arguments passed to subset methods.

### Functions

- `segReads`: `segReads` Constructor

- `segReadsList`: `segReadsList` Constructor

- `show,segReads-method`: show method

- `show,segReadsList-method`: show method

- `map`: map generic

- `map,segReads-method`: map method

- `map,segReadsList-method`: map method

- `length,segReadsList-method`: Return length of segReadsList

- `summary,segReadsList-method`: Summary method

- `summary,segReads-method`: Summary method

- `[,segReadsList,ANY,ANY,ANY-method`: Subset methods

- `[[,segReadsList,ANY,ANY-method`: Subset methods

### Note

segReads and segReadsList objects are not meant to be built via the constructors. The constructors are used in `segmentPICS`.

[Package PICS version 2.38.0 Index]