otherChildXICpp {DIAlignR} | R Documentation |
Get child chromatogram for other precursors using main precursor alignment
otherChildXICpp( l1, l2, kernelLen, polyOrd, mat, childTime, wRef = 0.5, splineMethod = "natural" )
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". |
(List) of chromatograms.
Shubham Gupta, shubh.gupta@mail.utoronto.ca ORCID: 0000-0003-3500-8152 License: (c) Author (2021) + MIT Date: 2021-01-08
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")