getChromSimMatCpp: Calculates similarity matrix of two fragment-ion chromatogram...

In DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description

Calculates similarity matrix of two fragment-ion chromatogram groups or extracted-ion chromatograms(XICs)

Usage

getChromSimMatCpp(
  l1,
  l2,
  normalization,
  simType,
  cosAngleThresh = 0.3,
  dotProdThresh = 0.96
)

Arguments

l1	(list) A list of vectors. Length should be same as of l2.
l2	(list) A list of vectors. Length should be same as of l1.
normalization	(char) A character string. Normalization must be selected from (L2, mean or none).
simType	(char) A character string. Similarity type must be selected from (dotProductMasked, dotProduct, cosineAngle, cosine2Angle, euclideanDist, covariance, correlation). Mask = s > quantile(s, dotProdThresh) AllowDotProd= [Mask × cosine2Angle + (1 - Mask)] > cosAngleThresh s_new= s × AllowDotProd
cosAngleThresh	(numeric) In simType = dotProductMasked mode, angular similarity should be higher than cosAngleThresh otherwise similarity is forced to zero.
dotProdThresh	(numeric) In simType = dotProductMasked mode, values in similarity matrix higher than dotProdThresh quantile are checked for angular similarity.

Value

s (matrix) Numeric similarity matrix. Rows and columns expresses seq1 and seq2, respectively.

Author(s)

Shubham Gupta, [e-mail] ORCID: 0000-0003-3500-8152 License: (c) Author (2019) + MIT Date: 2019-03-05

Examples

# Get similarity matrix of dummy chromatograms
r1 <- list(c(1.0,3.0,2.0,4.0), c(0.0,0.0,0.0,1.0), c(4.0,4.0,4.0,5.0))
r2 <- list(c(1.4,2.0,1.5,4.0), c(0.0,0.5,0.0,0.0), c(2.0,3.0,4.0,0.9))
round(getChromSimMatCpp(r1, r2, "L2", "dotProductMasked"), 3)
matrix(c(0.125, 0.162, 0.144, 0.208, 0.186, 0.240,
0.213, 0.313, 0.233, 0.273, 0.253, 0.346, 0.101, 0.208, 0.154, 0.273), 4, 4, byrow = FALSE)

round(getChromSimMatCpp(r1, r2, "L2", "dotProduct"), 3)
matrix(c(0.125, 0.162, 0.144, 0.208, 0.186,0.240, 0.213, 0.313, 0.233,
0.273, 0.253, 0.346, 0.101, 0.208, 0.154, 0.273), 4, 4, byrow = FALSE)

round(getChromSimMatCpp(r1, r2, "L2", "cosineAngle"), 3)
matrix(c(0.934, 0.999, 0.989, 0.986, 0.933, 0.989,
 0.983, 0.996, 0.994, 0.960, 0.995, 0.939, 0.450,
 0.761, 0.633, 0.772), 4, 4, byrow = FALSE)

round(getChromSimMatCpp(r1, r2, "L2", "cosine2Angle"), 3)
matrix(c(0.744, 0.998, 0.957, 0.944, 0.740, 0.956, 0.932,
0.985, 0.974, 0.842, 0.978, 0.764, -0.596, 0.158,
-0.200, 0.190), 4, 4, byrow = FALSE)

round(getChromSimMatCpp(r1, r2, "mean", "euclideanDist"), 3)
matrix(c(0.608, 0.614, 0.680, 0.434, 0.530, 0.742,
0.659, 0.641, 0.520, 0.541, 0.563, 0.511, 0.298,
0.375, 0.334, 0.355), 4, 4, byrow = FALSE)

round(getChromSimMatCpp(r1, r2, "L2", "covariance"), 3)
matrix(c(0.025, 0.028, 0.027, 0.028, 0.032, 0.034,
0.033, 0.034, 0.055, 0.051, 0.053, 0.051,
-0.004, 0.028, 0.012, 0.028), 4, 4, byrow = FALSE)

round(getChromSimMatCpp(r1, r2, "L2", "correlation"), 3)
matrix(c(0.874, 0.999, 0.974, 0.999, 0.923, 0.986, 0.993,
0.986, 0.991, 0.911, 0.990, 0.911, -0.065, 0.477,
0.214, 0.477), 4, 4, byrow = FALSE)

DIAlignR documentation built on Nov. 8, 2020, 8:22 p.m.