sliding_density: Calculate DIAS using sliding density method.

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

Description

Sliding density scores each segment in signature according to composition of nearby signature.

Usage

sliding_density(signature, oligos = NULL, window = 100, alpha = c(0.05,
  0.025, 0.01))

Arguments

signature	signature from get_signature function
oligos	either numeric or character vector of oligonucleotides that will be used. If nos specified, whole signature is used.
window	size of subset to the left
alpha	significance level of scoring intervals.

Details

Sliding density uses subset of signature centered around single segment and constructs density out of this subset. From this density, credibility intervals are constructed according to significance level alpha and DIAS score is calculated for single segment around which density is centered.

This differs from global density method as DIAS score is calculated only on centered segment, while in global density, DIAS score is calculated for every segment of signature from which density was constructed.

Parameter window does not specify whole size of subset taken, but only left and right part. That means that it takes a window left from central segment and window right. As first segment of signature doesn't have anything on left and the last segment of signature doesn't have anything on right, size of actuall subset range from (window+1) to (2*window + 1)

Value

DIAS score for given signature.

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