xtmgah/kataegisportal

KataegisPortal

KataegisPortal is an R package that provides utilities to detect and visualize the Kataegis events from single nucleotide variants (SNVs).

Installation

library(devtools)
install_github("MeichunCai/KataegisPortal")

How to use

# Load packages
library(KataegisPortal)
library(BSgenome)
library(BSgenome.Hsapiens.UCSC.hg19)

# Read in snv data
mutData <- "examples/mutData.txt"
mutData <- read.table(mutData, header = TRUE,sep = "\t",as.is = TRUE)
head(mutData)

# Covert to KataegisPortal input
mutSNP = mutSNP.input(mut.data = mutData,
			chr = "chr",
			pos = "pos",
			ref = "ref",
			alt = "alt",
			build = "hg19")

# Identify potential kataegis events
katPoint(mutSNP)

• weight.C>X: proportion of C>X mutations
• confidence: confidence degree of potential kataegis events (range: 0 to 3, 0 - a hypermutation with weight.C>X < 0.8; 1 - one hypermutation with weight.C>X >= 0.8 in a chromosome; 2 - two hypermutations with weight.C>X >= 0.8 in a chromosome; 3 - high confidence with three or more hypermutations with weight.C>X >= 0.8 in a chromosome)

# Identify potential kataegis events with annonation
library(ChIPseeker)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
katPoint(mutSNP,txdb = TxDb.Hsapiens.UCSC.hg19.knownGene)

# Plot intermutation distance to display kataegis or hyper mutated genomic regions
mutDis.plot(plot.data = mutSNP, sample="Test")

mutDis.plot(plot.data = mutSNP, sample="Test", chr = "chr2")

# Plot of flanking sequence of all C>X mutations or C>X mutations within a chromosome/chromosome arm
baseSpe.plot(plot.data = mutSNP, sample="Test")

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

References

• Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979-993, doi:10.1016/j.cell.2012.04.024 (2012).
• Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-421, doi:10.1038/nature12477 (2013).