plotLfcGC-methods {exomePeak2}R Documentation

Method plotLfcGC

Description

plotLfcGC plot the scatter plot between GC content and the (differential) modification LFCs.

Usage

plotLfcGC(
  sep,
  bsgenome = NULL,
  txdb = NULL,
  save_pdf_prefix = NULL,
  point_size = 0.05,
  xlim = c(0.2, 0.9),
  fragment_length = 100,
  binding_length = 25,
  effective_GC = FALSE,
  save_dir = "."
)

## S4 method for signature 'SummarizedExomePeak'
plotLfcGC(
  sep,
  bsgenome = NULL,
  txdb = NULL,
  save_pdf_prefix = NULL,
  point_size = 0.05,
  xlim = c(0.2, 0.9),
  fragment_length = 100,
  binding_length = 25,
  effective_GC = FALSE,
  save_dir = "."
)

Arguments

sep

a SummarizedExomePeak object.

bsgenome

a BSgenome object for the genome sequence, it could be the name of the reference genome recognized by getBSgenome.

txdb

a TxDb object for the transcript annotation, it could be the name of the reference genome recognized by makeTxDbFromUCSC.

save_pdf_prefix

a character, if provided, a pdf file with the given name will be saved under the current directory; Default = NULL.

point_size

a numeric value for the point size of the scatter plot; Default = 0.05.

xlim

a numeric vector for the range of x-axis of the plot; Default = c(0.2,0.9).

fragment_length

a numeric value for the expected fragment length in the RNA-seq library; Default = 100.

binding_length

a numeric value for the expected antibody binding length in IP samples; Default = 25.

effective_GC

a logical value of whether to calculate the weighted GC content by the probability of reads alignment; default = FALSE.

save_dir

a character for the directory to save the plot; default ".".

Details

By default, this function will generate a scatter plot between GC content and the log2FC value. The significant modification sites will be lebeled in different colours.

Value

a ggplot object.

Examples



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

sep <- readRDS(f1)

### Visualize the relationship between GC content and the (differential) LFC
plotLfcGC(sep)


[Package exomePeak2 version 1.6.1 Index]