mutDis.plot: function mutDis.plot() to plot intermutation distance

In MeichunCai/KataegisPortal: Detection and Visualization of Kataegis

Description

Plot intermutation distance to display kataegis or hyper mutated genomic regions.

Usage

mutDis.plot(plot.data, sample = "sample", chr = NULL, color = NULL, min.mut = 6, max.dis = 1000)

Arguments

plot.data	An object as returned by the 'mutSNP.input' function.
sample	Name of sample [default: sample].
chr	Chromosome for which the plot will be generated [default: 1:24].
color	Colour to show the mutations ("C>A", "C>G", "C>T", "T>A", "T>C", "T>G").
min.mut	Minimum number of consecutive mutations is used to identify potential kataegis events [default: 6].
max.dis	Maximum number of bases between two mutations is used to identify potential kataegis events [default: 1000].

Examples

library(KataegisPortal)
library(BSgenome)
library(BSgenome.Hsapiens.UCSC.hg19)
mutData <- "examples/mutData.txt"
mutData <- read.table(mutData, header = TRUE,sep = "\t",as.is = TRUE)
mutSNP = mutSNP.input(mut.data = mutData,
			chr = "chr",
			pos = "pos",
			ref = "ref",
			alt = "alt",
			build = "hg19")
mutDis.plot(plot.data = mutSNP, sample="Test", chr = c(1:23))

MeichunCai/KataegisPortal documentation built on July 16, 2020, 8:59 p.m.