plotExonLength-methods {exomePeak2}R Documentation

Method plotExonLength

Description

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

Usage

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 = "."
)

Arguments

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 = ".".

Details

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.

Value

a ggplot object

Examples


### 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)


[Package exomePeak2 version 1.6.1 Index]