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

Description Usage Arguments Details Value Examples

This function plot the distribution of the exon length for peaks containing exons.

plotExonLength(
  sep,
  txdb = NULL,
  save_pdf_prefix = NULL,
  include_control_regions = TRUE,
  save_dir = "."
)

## S4 method for signature 'SummarizedExomePeak'
plotExonLength(
  sep,
  txdb = NULL,
  save_pdf_prefix = NULL,
  include_control_regions = TRUE,
  save_dir = "."
)

`sep`	a `SummarizedExomePeak` object.
`txdb`	a `TxDb` object containing the transcript annotation.
`save_pdf_prefix`	a `character` if provided, a pdf file with the given name will be saved under the current working directory.
`include_control_regions`	a `logical` for whether to include the control regions or not; Default `= TRUE`.
`save_dir`	a `character` for the directory to save the plot; Default `= "."`.

If the SummarizedExomePeaks object contains LFC statistics, the significantly modified peaks with IP to input log2FC > 0 and GLM Wald test padj < .05 will be plotted .

If the SummarizedExomePeaks object contains interactive LFC statistics, both the hyper modification and hypo modification peaks with GLM Wald test p values < .05 will be plotted.

a ggplot object

### Make TxDb object from the gff file
library(GenomicFeatures)
GENE_ANNO_GTF = system.file("extdata", "example.gtf", package="exomePeak2")

txdb <- makeTxDbFromGFF(GENE_ANNO_GTF)

### Load the example SummarizedExomPeak object
f1 = system.file("extdata", "sep_ex_mod.rds", package="exomePeak2")

sep <- readRDS(f1)

### Visualize the linear relationships between GC content and normalized reads count under different regions
plotExonLength(sep,txdb)