/KataegisPortal_CHM13

An R package for detecting and visualizing Kataegis events

Primary LanguageR

Support CHM13

you need to build your own BSgenome and install it or you can download it directly and install it locally. https://drive.google.com/file/d/1_aezGIwybIFoedRTqEC2aBTVXP5Jyhu-/view?usp=sharing

then

library(BSgenome.Hsapiens.CHM13)
mutSNP = mutSNP.input(mut.data = mutData,
			chr = "chr",
			pos = "pos",
			ref = "ref",
			alt = "alt",
			build = "CHM13")

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 <- system.file("examples", "mutData.txt", package="KataegisPortal")
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)

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  • 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)

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

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

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# 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")

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

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Citation

  • Xia Yin, Rui Bi, Pengfei Ma, Shengzhe Zhang, Yang Zhang, Yunheng Sun, Yi Zhang, Ying Jing, Minhua Yu, Wenjing Wang, Li Tan, Wen Di #, Guanglei Zhuang #, Mei-Chun Cai #. Multiregion whole-genome sequencing depicts intratumor heterogeneity and punctuated evolution in ovarian clear cell carcinoma. Journal of Medical Genetics. 2019 Dec 20;jmedgenet-2019-106418. doi: 10.1136/jmedgenet-2019-106418.