gaiaCNVplot: Creates a plot for GAIA output (all significant aberrant...

In TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Description

This function is a auxiliary function to visualize GAIA output (all significant aberrant regions.)

Usage

gaiaCNVplot(calls, threshold = 0.01)

Arguments

calls	A matrix with the following columns: Chromossome, Aberration Kind Region Start, Region End, Region Size and score
threshold	Score threshold (orange horizontal line in the plot)

Value

A plot with all significant aberrant regions.

Examples

call <- data.frame("Chromossome" = rep(9,100),
                   "Aberration Kind" = rep(c(-2,-1,0,1,2),20),
                   "Region Start [bp]" = 18259823:18259922,
                   "Region End [bp]" = 18259823:18259922,
                   "score" = rep(c(1,2,3,4),25))
 gaiaCNVplot(call,threshold = 0.01)
 call <- data.frame("Chromossome" = rep(c(1,9),50),
                    "Aberration Kind" = rep(c(-2,-1,0,1,2),20),
                    "Region Start [bp]" = 18259823:18259922,
                    "Region End [bp]" = 18259823:18259922,
                    "score" = rep(c(1,2,3,4),25))
 gaiaCNVplot(call,threshold = 0.01)

TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.