get.nucleotide.chunk.counts {SeqKat}

Get Nucleotide Chunk Counts

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
	);