otherChildXICpp: Get child chromatogram for other precursors using main...
In shubham1637/DIAlign: Dynamic Programming Based Alignment of MS2 Chromatograms

otherChildXICpp

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")

shubham1637/DIAlign documentation built on March 27, 2023, 7:12 a.m.