rainfallPlot: Rainfall plot to display hyper mutated genomic regions.

Description Usage Arguments Details Value

View source: R/rainfallPlot.R

Description

Plots inter variant distance as a function of genomic locus.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
rainfallPlot(
  maf,
  tsb = NULL,
  detectChangePoints = FALSE,
  ref.build = "hg19",
  color = NULL,
  savePlot = FALSE,
  width = 6,
  height = 3,
  fontSize = 1.2,
  pointSize = 0.4
)

Arguments

maf

an MAF object generated by read.maf. Required.

tsb

specify sample names (Tumor_Sample_Barcodes) for which plotting has to be done. If NULL, draws plot for most mutated sample.

detectChangePoints

If TRUE, detectes genomic change points where potential kataegis are formed. Results are written to an output tab delimted file.

ref.build

Reference build for chromosome sizes. Can be hg18, hg19 or hg38. Default hg19.

color

named vector of colors for each coversion class.

savePlot

If TRUE plot is saved to output pdf. Default FALSE.

width

width of plot to be saved.

height

height of plot to be saved.

fontSize

Default 12.

pointSize

Default 0.8.

Details

If 'detectChangePoints“ is set to TRUE, this function will identify Kataegis loci. Kategis detection algorithm by Moritz Goretzky at WWU Munster, which exploits the definition of Kategis (six consecutive mutations with an avg. distance of 1000bp ) to idetify hyper mutated genomic loci. Algorithm starts with a double-ended queue to which six consecutive mutations are added and their average intermutation distance is calculated. If the average intermutation distance is larger than 1000, one element is added at the back of the queue and one is removed from the front. If the average intermutation distance is less or equal to 1000, further mutations are added until the average intermutation distance is larger than 1000. After that all mutations in the double-ended queue are written into output as one kataegis and the double-ended queue is reinitialized with six mutations.

Value

Results are written to an output file with suffix changePoints.tsv


thesushantpatil/maftools documentation built on May 18, 2020, 9:54 p.m.