eye_of_storm: Calculate DIAS using Eye of storm variant of sliding density...
In J-Moravec/sighunt: Tool for horizontal transfer detection

Description Usage Arguments Details Value

Eye of storm score each segment in signature according to composition of local signature but without segment itself and some closest segments around it.

1 2	eye_of_storm(signature, oligos = NULL, window = 100, eye = 5, alpha = c(0.05, 0.025, 0.01))

`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
`eye`	number of segments around centered segment which are excluded from density estimation.
`alpha`	significance level of scoring intervals.

Eye of storm is similar to sliding density, it uses subset of signature centered around single segment, removes mentioned segment and some other negihbouring segments specified by eye parameter and then produce density from this filtered subset of signature. Segment around which this subset is centered is then scored based on credibility interval constructed from estimated density.

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)

Parameter eye define number of segments in signature (single number that show frequency of oligonucleotide in part of sequence) that are excluded from density estimation.

DIAS score for given signature.

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