SeqKat (version 0.0.8)

get.nucleotide.chunk.counts: 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

Examples

# NOT RUN {
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
	);
# }