getGlobalAlignMaskCpp: Outputs a mask for constraining similarity matrix
In shubham1637/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

getGlobalAlignMaskCpp

R Documentation

Outputs a mask for constraining similarity matrix

Description

This function takes in timeVectors from both runs, global-fit mapped values of end-points of first time vector and sample-length of window of no constraining. Outside of window, all elements of matrix are either equally weighted or weighted proportional to distance from window-boundry.

Usage

getGlobalAlignMaskCpp(tA, tB, tBp, noBeef = 50L, hardConstrain = FALSE)

Arguments

`tA`	(numeric) This vector has equally spaced timepoints of XIC A.
`tB`	(numeric) This vector has equally spaced timepoints of XIC B.
`tBp`	(numeric) mapping of tA to run B using some global fit.
`noBeef`	(integer) It defines the distance from the global fit, upto which no penalization is performed. The window length = 2*noBeef.
`hardConstrain`	(logical) if false; indices farther from noBeef distance are filled with distance from linear fit line.

Value

mask (matrix) A numeric matrix.

Author(s)

Shubham Gupta, shubh.gupta@mail.utoronto.ca ORCID: 0000-0003-3500-8152 License: (c) Author (2019) + MIT Date: 2019-03-08

Examples

tA <- c(1707.6, 1711, 1714.5, 1717.9, 1721.3, 1724.7, 1728.1, 1731.5, 1734.9, 1738.4)
tB <- c(1765.7, 1769.1, 1772.5, 1775.9, 1779.3, 1782.7, 1786.2, 1789.6, 1793, 1796.4)
tBp <- c(1786.9, 1790.35, 1793.9, 1797.36, 1800.81, 1804.26, 1807.71, 1811.17, 1814.62, 1818.17)
noBeef <- 1
mask <- getGlobalAlignMaskCpp(tA, tB, tBp, noBeef, FALSE)
round(mask, 3)
matrix(c( 5.215,4.218,4.221,2.225,1.228,0,0,0,0.788, 1.785,
6.226,5.230,4.233,3.236,2.239,1.243,0,0,0, 0.774), nrow = 2, ncol = 10, byrow = FALSE)
#image(mask) # A is on x-axis, B is on y-axis

shubham1637/DIAlignR documentation built on March 29, 2023, 8:45 p.m.