childXIC {DIAlignR} | R Documentation

## Get a child chromatogram from parents

### Description

Internal gaps in reference chromatogram and corresponding indices in experiment chromatogram are discarded while merging both chromatogram to obtain a child chromatogram.

### Usage

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

### Arguments

`XIC.ref` | (data-frame) extracted ion chromatogram from reference run. Must not contain missing values.
`XIC.eXp` | (data-frame) extracted ion chromatogram from experiment run. Must not contain missing values.
`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 chromatogram. The second element is aligned parent time-vectors.

### time-merging

There are three startegies for calculating time to keep sampling rate equal to parents:
- Use reference time.
- Average time (Non-gap region will have parent's sampling rate).
- Start/end with the average then fixed sampling rate.

### 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

`mergeXIC, alignedXIC, childXICs`

### 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_
    ## Not run:
    plot(childXIC(XICs.ref[[1]], XICs.eXp[[1]], alignedIndices)[[1]], type = 'l')

    ## End(Not run)

[Package DIAlignR version 2.2.0 Index]