getGlobalAlignMaskCpp {DIAlignR} | 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

[Package DIAlignR version 2.2.0 Index]