baseSpe.plot: function baseSpe.plot() to plot C>X mutations base spectum

In MeichunCai/KataegisPortal: Detection and Visualization of Kataegis

Description

Plot of flanking sequence of all C>X mutations or C>X mutations within a chromosome/chromosome arm.

Usage

baseSpe.plot(plot.data, sample = "sample", chr = NULL, arm = NULL, color = NULL, k = NULL)

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].
arm	Chromosome arm for which the plot will be generated. Can be p or q. [default: NULL].
color	Colour to show the bases ("A", "C", "G", "T").
k	'K'-mer bases of flanking sequence of mutated base [default: the same as 'mutSNP.input' function].

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")
baseSpe.plot(plot.data = mutSNP, sample="Test", chr = "chr2",arm="q")

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