SummarizedExomePeak-class: SummarizedExomePeak

In exomePeak2: Bias Awared Peak Calling and Quantification for MeRIP-Seq

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)

exomePeak2 documentation built on Nov. 8, 2020, 5:27 p.m.