get.nucleotide.chunk.counts: Get Nucleotide Chunk Counts

In SeqKat: Detection of Kataegis

Description

Obtain counts for all possible trinucleotides within a specified genomic region

Usage

get.nucleotide.chunk.counts(key, chr, upstream = 1, downstream = 1,
  start = 1, end = -1)

Arguments

key	List of specify trinucleotides to count
chr	Chromosome
upstream	Length upstream to read
downstream	Length downstream to read
start	Starting position
end	Ending position

Author(s)

Fouad Yousif

Examples

example.ref.dir <- paste0(
	path.package("SeqKat"),
	"/extdata/test/ref/"
	);

bases.raw <- c('A','C','G','T','N');
tri.types.raw <- c(
	outer(
		c(outer(bases.raw, bases.raw, function(x, y) paste0(x,y))),
		bases.raw, function(x, y) paste0(x,y))
	);
tri.types.raw <- sort(tri.types.raw);
get.nucleotide.chunk.counts(
	tri.types.raw,
	file.path(example.ref.dir, 'chr4.fa'),
	upstream = 1,
	downstream = 1,
	start = 1,
	end = -1
	);

SeqKat documentation built on March 13, 2020, 1:59 a.m.