SummarizedExomePeak-class {exomePeak2} | R Documentation

## SummarizedExomePeak

### Description

An S4 object defined in exomePeak2 that summarizes the information of modification peaks/sites, reads counts, size factors, GC contents, and the LFC related statistics.

This class contains SummarizedExperiment.

### Usage

    SummarizedExomePeak(...)

### Arguments

`...` | arguments passed to `new()`.

### Details

Constructors:

The `SummarizedExomePeak` object can be constructed by 3 functions.

1. SummarizedExomePeak

2. exomePeakCalling

3. exomePeak2

Accessors:

The `SummarizedExomePeak` object share all the accessors with the SummarizedExperiment class.

It has 2 additional accessors:

1. GCsizeFactors

2. exomePeak2Results

### Value

SummarizedExomePeak object

### Examples

    # Generate the SummarizedExomePeak object by peak calling

    GENE_ANNO_GTF = system.file("extdata", "example.gtf", package="exomePeak2")

    f1 = system.file("extdata", "IP1.bam", package="exomePeak2")
    f2 = system.file("extdata", "IP2.bam", package="exomePeak2")
    f3 = system.file("extdata", "IP3.bam", package="exomePeak2")
    f4 = system.file("extdata", "IP4.bam", package="exomePeak2")
    IP_BAM = c(f1,f2,f3,f4)
    f1 = system.file("extdata", "Input1.bam", package="exomePeak2")
    f2 = system.file("extdata", "Input2.bam", package="exomePeak2")
    f3 = system.file("extdata", "Input3.bam", package="exomePeak2")
    INPUT_BAM = c(f1,f2,f3)

    sep <- exomePeak2(bam_ip = IP_BAM,
                      bam_input = INPUT_BAM,
                      gff_dir = GENE_ANNO_GTF,
                      genome = "hg19",
                      paired_end = FALSE)

    #Access to the slots in the SummarizedExomePeak object

    ## Access to reads count
    assays(sep)

    ## Access to the sequencing depth size factors and experimental design
    colData(sep)

    ## Access to the GC content and feature length information
    elementMetadata(sep)

    ## Access to the genomic locations of the modification peaks/sites and the background control regions
    rowRanges(sep)

    ## Access to the feature specific size factors
    GCsizeFactors(sep)

    ## Access to the statistics on (differential) modification LFC
    exomePeak2Results(sep)

[Package exomePeak2 version 0.99.98 Index]