childXICs {DIAlignR} | R Documentation

## Get child chromatograms from parents

### Description

Get child chromatograms from parents

### Usage

    childXICs(
      XICs.ref,
      XICs.eXp,
      alignedIndices,
      method = "spline",
      polyOrd = 4,
      kernelLen = 9,
      splineMethod = "fmm",
      wRef = 0.5,
      mergeStrategy = "avg",
      keepFlanks = TRUE
    )

### Arguments

`XICs.ref` | (list of data-frames) extracted ion chromatograms from reference run.
`XICs.eXp` | (list of data-frames) extracted ion chromatograms from experiment run.
`alignedIndices` | (data-frame) must have two columns "indexAligned.ref" and "indexAligned.eXp".
`method` | (string) must be either "spline", "sgolay" or "linear".
`polyOrd` | (integer) must be less than kernelLen.
`kernelLen` | (integer) must be an odd integer.
`splineMethod` | (string) must be either "fmm" or "natural".
`wRef` | (numeric) Weight of the reference XIC. Must be between 0 and 1.
`mergeStrategy` | (string) must be either ref, avg, refStart or refEnd.
`keepFlanks` | (logical) TRUE: Flanking chromatogram is not removed.

### Value

(list) the first element is a list of chromatograms. The second element is aligned parent time-vectors.

### Author(s)

Shubham Gupta, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-05-23

### See Also

`childXIC, mergeXIC`

### Examples

    data(XIC_QFNNTDIVLLEDFQK_3_DIAlignR, package="DIAlignR")
    data(alignObj_DIAlignR, package="DIAlignR")
    XICs.ref <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]]
    XICs.eXp <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]]
    alignedIndices <- cbind(alignObj_DIAlignR@indexA_aligned, alignObj_DIAlignR@indexB_aligned)
    colnames(alignedIndices) <- c("indexAligned.ref", "indexAligned.eXp")
    alignedIndices[, 1:2][alignedIndices[, 1:2] == 0] <- NA_integer_
    newXICs <- childXICs(XICs.ref, XICs.eXp, alignedIndices)[[1]]
    plotXICgroup(XICs.ref)
    plotXICgroup(newXICs)

[Package DIAlignR version 2.2.0 Index]