otherChildXICpp {DIAlignR} | R Documentation

## Get child chromatogram for other precursors using main precursor alignment

### Description

Get child chromatogram for other precursors using main precursor alignment

### Usage

    otherChildXICpp(
      l1,
      l2,
      kernelLen,
      polyOrd,
      mat,
      childTime,
      wRef = 0.5,
      splineMethod = "natural"
    )

### Arguments

`l1` | (list) A list of numeric matrix of two columns. l1 and l2 should have same length.
`l2` | (list) A list of numeric matrix of two columns. l1 and l2 should have same length.
`kernelLen` | (integer) length of filter. Must be an odd number.
`polyOrd` | (integer) TRUE: remove background from peak signal using estimated noise levels.
`mat` | (matrix) aligned time and child time from the main precursor.
`childTime` | (numeric) iime vector from the child chromatogram.
`wRef` | (numeric) Weight of the reference XIC. Must be between 0 and 1.
`splineMethod` | (string) must be either "fmm" or "natural".

### Value

(List) of chromatograms.

### Author(s)

Shubham Gupta, shubh.gupta@mail.utoronto.ca ORCID: 0000-0003-3500-8152 License: (c) Author (2021) + MIT Date: 2021-01-08

### Examples

    data(XIC_QFNNTDIVLLEDFQK_3_DIAlignR, package="DIAlignR")
    XICs <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR
    XICs.ref <- lapply(XICs[["hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]], as.matrix)
    XICs.eXp <- lapply(XICs[["hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]], as.matrix)
    Bp <- seq(4964.752, 5565.462, length.out = nrow(XICs.ref[[1]]))
    chrom <- getChildXICpp(XICs.ref, XICs.eXp, 11L, 4L, alignType = "hybrid", adaptiveRT = 77.82315,
     normalization = "mean", simType = "dotProductMasked", Bp = Bp,
     goFactor = 0.125, geFactor = 40, cosAngleThresh = 0.3, OverlapAlignment = TRUE,
     dotProdThresh = 0.96, gapQuantile = 0.5, hardConstrain = FALSE, samples4gradient = 100,
     wRef = 0.5, keepFlanks= TRUE)
    chrom2 <- otherChildXICpp(XICs.ref, XICs.eXp, 11L, 4L, chrom[[2]], chrom[[1]][[1]][,1],
    0.5, "natural")

[Package DIAlignR version 2.2.0 Index]