global_density: Calculate DIAS using global density method

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

Description

Function calculate DIAS score from signature using global density method.

Usage

global_density(signature, oligos = NULL, alpha = c(0.05, 0.025, 0.01))

Arguments

signature	signature from get_signature function
oligos	either numeric vector or character vector of oligonucleotides that will be used. If not specified, whole signature is used.
alpha	significance level of scoring intervals.

Details

First, signature is filtered and quality is removed. If oligos were specified, only specified oligos (either columns, if oligos was numeric vector, or specific oligonucleotides, if oligos was character vector) are kept. Then global density for all retained oligonucleotide is calculated and each window of signature is scored if it falls to confidence interval defined by alpha. Then all DIAS from all oligonucleotides are summed and final DIAS is returned.

Value

DIAS score for given signature.

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