mutSNP.input: function mutSNP.input() for data transformation

In MeichunCai/KataegisPortal: Detection and Visualization of Kataegis

Description

Makes the contexts useable in katPoint(), mutDis.plot() and baseSpe.plot().

Usage

mutSNP.input(mut.data, chr = "chr", pos = "pos", ref = "ref", alt = "alt", build = NULL, k = 10)

Arguments

mut.data	A data frame of mutation(SNV) file.
chr	Column name in the mutation file corresponding to the chromosome.
pos	Column name in the mutation file corresponding to the mutation position.
ref	Column name in the mutation file corresponding to the reference base.
alt	Column name in the mutation file corresponding to the alternate base.
build	Reference build for chromosome sizes. Can be hg18, hg19 or hg38.
k	'K'-mer bases of flanking sequence of mutated base [default: 10].

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")

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