DRrefit_plot: DRrefit_plot

In bioinformatic-seragnoli/BOBaFIT: Refitting diploid region profiles using a clustering procedure

DRrefit_plot

Description

The function plot the copy number profile before and after DRrefit recalibration

Usage

DRrefit_plot(
  corrected_segments,
  DRrefit_report,
  plot_viewer = F,
  plot_save = F,
  plot_format = "png",
  plot_path
)

Arguments

corrected_segments	DRrefit output dataframe.
DRrefit_report	DRrefit output dataframe.
plot_viewer	Logical parameter. When it is TRUE, the function print the output plot in the R viewer.By default is FALSE.
plot_save	Logical parameter. When it is TRUE, the function save the plot in the chosen path and format. By default is FALSE.
plot_format	File format for the output plots (accepts "png", "jpg", "pdf", "tiff"). By default is "png"
plot_path	Path to save output plots.

Value

Return the sample copy number profile before and after DRrefit recalibration. The function can output the figure in the R viewer on save it in a specific path.

Examples

data("TCGA_BRCA_CN_segments")

chr_list <- c("10q","11p","12p","19q","1p","21q","2q","3p","4p","4q","6p","6q","7p" )

results <- DRrefit(segments_chort = TCGA_BRCA_CN_segments, chrlist = chr_list)
                   
my_segments <- results$corrected_segments
my_report <- results$report

DRrefit_plot(corrected_segments = my_segments,
             DRrefit_report = my_report, 
             plot_viewer= FALSE, 
             plot_save = FALSE)

bioinformatic-seragnoli/BOBaFIT documentation built on Jan. 29, 2024, 10:27 a.m.