retrievePeaks {chromswitch} | R Documentation

## retrievePeaks

### Description

Given a peak calls for a set of samples, for each sample, get the peaks which overlap a specified genomic region of interest. Typically, this corresponds to the region for which we will construct a feature matrix representing peaks in the region in order to call a chromatin state switch.

### Usage

    retrievePeaks(peaks, metadata, region)

### Arguments

`peaks` | List of GRanges objects storing peak calls for each sample
`metadata` | Dataframe with a column "Sample" which stores the sample identifiers, and at least one column, titled by the histone mark or ChIP-seq target, storing paths to the BED files containing peak calls
`region` | GRanges object specifying one genomic region, the query region

### Value

LocalPeaks object as described in `LocalPeaks`

### Examples

    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)

    retrievePeaks(H3K4me3,
        metadata = metadata,
        region = GRanges(seqnames = "chr19",
        ranges = IRanges(start = 54924104, end = 54929104)))

[Package chromswitch version 1.2.1 Index]