getBaseGapPenaltyCpp: Calculates gap penalty for dynamic programming based...
In DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms
Description
Usage
Arguments
Value
Author(s)
Examples
Description
This function outputs base gap-penalty depending on SimType used. In case of getting base gap-penalty
from similarity matrix distribution, gapQuantile will be used to pick the value.
Usage
1
getBaseGapPenaltyCpp(sim, SimType, gapQuantile = 0.5)
Arguments
sim
(matrix) A numeric matrix. Input similarity matrix.
SimType
(char) A character string. Similarity type must be selected from (dotProductMasked, dotProduct, cosineAngle, cosine2Angle, euclideanDist, covariance, correlation).
gapQuantile
(numeric) Must be between 0 and 1.
Value
baseGapPenalty (numeric).
Author(s)
Shubham Gupta, shubh.gupta@mail.utoronto.ca
ORCID: 0000-0003-3500-8152
License: (c) Author (2019) + MIT
Date: 2019-03-08
Examples
1
2
3
sim <- matrix(c(-12, 1.0, 12, -2.3, -2, -2, 1.07, -2, 1.80, 2, 22, 42, -2, -1.5, -2, 10), 4, 4,
byrow = FALSE)
getBaseGapPenaltyCpp(sim, "dotProductMasked", 0.5) # -0.25
DIAlignR documentation built on Nov. 8, 2020, 8:22 p.m.
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Description Usage Arguments Value Author(s) Examples
Description
This function outputs base gap-penalty depending on SimType used. In case of getting base gap-penalty from similarity matrix distribution, gapQuantile will be used to pick the value.
Usage
1 | getBaseGapPenaltyCpp(sim, SimType, gapQuantile = 0.5)
|
Arguments
sim |
(matrix) A numeric matrix. Input similarity matrix. |
SimType |
(char) A character string. Similarity type must be selected from (dotProductMasked, dotProduct, cosineAngle, cosine2Angle, euclideanDist, covariance, correlation). |
gapQuantile |
(numeric) Must be between 0 and 1. |
Value
baseGapPenalty (numeric).
Author(s)
Shubham Gupta, shubh.gupta@mail.utoronto.ca ORCID: 0000-0003-3500-8152 License: (c) Author (2019) + MIT Date: 2019-03-08
Examples
1 2 3 | sim <- matrix(c(-12, 1.0, 12, -2.3, -2, -2, 1.07, -2, 1.80, 2, 22, 42, -2, -1.5, -2, 10), 4, 4,
byrow = FALSE)
getBaseGapPenaltyCpp(sim, "dotProductMasked", 0.5) # -0.25
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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