LocalPeaks-class {chromswitch} | R Documentation

## LocalPeaks

### Description

The LocalPeaks class is a container for the peaks for one or more marks for a set of samples in a specific genomic region of interest, as well as the genomic region itself, and the sample IDs. These components are needed to convert sets of peaks into rectangular feature-by-sample matrices which we can then use for downstream analysis - and in particular, as input to a clustering algorithm in order to call a chromatin state switch.

### Usage

    ## S4 method for signature 'LocalPeaks'
    region(x)
    ## S4 method for signature 'LocalPeaks'
    samples(object)
    ## S4 method for signature 'LocalPeaks'
    peaks(x)

### Arguments

`x` | LocalPeaks object, as returned by `retrievePeaks`
`object` | LocalPeaks object, as returned by `retrievePeaks`

### Value

LocalPeaks object

### Slots

`region`

  A GRanges object specifying one genomic region, the query region

`peaks`

  List of lists of GRanges objects. Each outer list stores peaks for each sample for one mark in `region`.

`samples`

  Character vector with sample identifiers.

### Methods

`region`:

  Access region slot of `LocalPeaks` object.

`samples`:

  Access samples slot of `LocalPeaks` object.

`peaks`:

  Access peaks slot of `LocalPeaks` object.

### Examples

    # Assemble dataset
    samples <- c("E068", "E071", "E074", "E101", "E102", "E110")
    bedfiles <- system.file("extdata", paste0(samples, ".H3K4me3.bed"),
    package = "chromswitch")

    metadata <- data.frame(Sample = samples,
        H3K4me3 = bedfiles,
        stringsAsFactors = FALSE)

    # Obtain a LocalPeaks object by retrieving the peaks in the query region
    lpk <- retrievePeaks(H3K4me3,
        metadata = metadata,
        region = GRanges(seqnames = "chr19",
        ranges = IRanges(start = 54924104, end = 54929104)))

    # lpk now stores the query region, samples, and associated peaks overlapping
    # the query region

    # Get the samples from the object
    samples(lpk)

    # Get the query region associated with the object
    region(lpk)

    # Get the set of peaks in each sample which overlap with the query region
    peaks(lpk)

[Package chromswitch version 1.8.0 Index]