mutation-distribution: Distributions of mutational locations.

In SomaticSignatures: Somatic Signatures

Description

Summary and plotting function for characterizing the distributions of mutations along the genome.

Usage

mutationDistance(x)

plotRainfall(x, group, size = 2, alpha = 0.5, space.skip = 0, ...)

Arguments

x	A 'GRanges' or 'VRanges' object [required].
group	The variable name for color groups [optional].
size	Point size [default: 2]
alpha	Alpha value for points [default: 0.5]
space.skip	Space between chromosomes, as defined by 'plotGrandLinear' [default: 0]
...	Additional arguments passed to 'plotGrandLinear'

Value

• mutationDensityThe position-sorted GRanges 'x' with the additional column 'distance', specifying the distance from the previous mutation (or the beginning of the chromosome if it happens to be the first mutation on the chromosome.)

• plotRainfallObject of class 'ggbio', as returned by 'plotGrandLinear'.

See Also

plotGrandLinear from the 'ggbio' package

Examples

library(GenomicRanges)
library(IRanges)

set.seed(1)
chr_len = 100
gr = GRanges(rep(1:3, each = 10),
  IRanges(start = sample.int(chr_len, 30, replace = FALSE), width = 1),
  mutation = sample(c("A", "C", "G", "T"), 30, replace = TRUE))
seqlengths(gr) = rep(chr_len, 3)

p = plotRainfall(gr)
print(p)

SomaticSignatures documentation built on Nov. 8, 2020, 5:52 p.m.