katPoint: function katPoint() to identify potential kataegis events

In MeichunCai/KataegisPortal: Detection and Visualization of Kataegis

Description

Identify potential kataegis events

Usage

katPoint(data, sample = "sample", min.mut = 6, max.dis = 1000, txdb = NULL)

Arguments

data	An object as returned by the 'mutSNP.input' function.
sample	Name of sample [default: sample].
min.mut	Minimum number of consecutive mutations is used to identify potential kataegis events[default: 6].
max.dis	Maximum number of bases between two mutations is used to identify potential kataegis events [default: 1000].
txdb	An annotation databases, e.g. TxDb.Hsapiens.UCSC.hg19.knownGene [default: NULL].

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")
library(ChIPseeker)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
katPoint(mutSNP,txdb = TxDb.Hsapiens.UCSC.hg19.knownGene)

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