pileup_peak {FunChIP} | R Documentation

## Computing read counts on a GRanges object.

### Description

Given a GRanges object and the path of a .bam file, it creates the corresponding pileup, containing the read counts on each nucleotide of the peaks of the GRanges object. Reads can be extended to a length `d`, which is an estimate of the length of the sequencing fragment. See the function compute_fragments_length for details. For each peak this method creates a vector containing these counts, i.e. the coverage function for the extended reads along the whole peak.

### Usage

    ## S4 method for signature 'GRanges'
    pileup_peak(object, bamf = NULL, d = NULL)

### Arguments

`object` | GRanges object containing the genomic coordinates of the peaks.
`bamf` | Path to the .bam file used to compute the coverage function. The associated .bam.bai index file must also be present.
`d` | integer. Total length of the fragments. Positive and negative reads are extended in their 3' direction. Default is NULL; this value can be estimated by compute_fragments_length.

### Value

the GRanges `object` with the new metadata column `counts` containing the coverage functions of the peaks.

### Author(s)

Alice Parodi, Marco J. Morelli, Laura M. Sangalli, Piercesare Secchi, Simone Vantini

### Examples

    # load the data
    # GRanges object

    data(GR)

    # import the .bam file

    bamf <- system.file("extdata", "test.bam", package="FunChIP",
                          mustWork=TRUE)

    # extract the first 10 peaks of the GRange
    # and compute the corresponding read counts
    # with fragment length 160.

    peaks <- pileup_peak(GR[1:10], bamf, d = 160)

[Package FunChIP version 1.13.0 Index]