get_signature: Get signature

In J-Moravec/sighunt: Tool for horizontal transfer detection

Description

Get signature for sequence. Signature is frequency of oligonucleotides computed for smaller overlapping subsets – windows. Function get_signature will partition sequence into individual windows, neighbouring windows overlap by window-step. For these windows, frequency of oligonucleotides is computed as count of oligonucleotide divided by maximum number of oligonucleotides of given length in window.

Usage

get_signature(sequence, oligos, window = 5000, step = 1000, file = NULL)

Arguments

sequence	string of DNA bases (ACGT)
oligos	character (or character vector) of oligonucleotide.
window	size of windows on which frequency is calculated
step	amount of bases by which each window is moved #TODO nonsense, better description
file	If specified, output will be piped file (or connection) instead

Details

Quality of sequence is also outputted, this is computed as frequency of non-ACGT characters.

Value

matrix of frequencies of oligos with quality of sequence

J-Moravec/sighunt documentation built on May 7, 2019, 6:46 a.m.