SummarizedExomePeak-class {exomePeak2} | R Documentation |
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.
SummarizedExomePeak(...)
... |
arguments passed to |
Constructors:
The SummarizedExomePeak
object can be constructed by 3 functions.
Accessors:
The SummarizedExomePeak
object share all the accessors with the SummarizedExperiment class.
It has 2 additional accessors:
SummarizedExomePeak object
# 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)