alignedXIC {DIAlignR} | R Documentation

## Create an aligned chromatogram

### Description

Modifies chromatogram to have the same length as indices. Imputes missing values with appropriate method. Time and intensity for the flanking missing indices are set as NA.

### Usage

    alignedXIC(
      XIC,
      indices,
      method = "spline",
      polyOrd = 4,
      kernelLen = 9,
      splineMethod = "fmm"
    )

### Arguments

`XIC` | (data-frame) first column is time, second column is intensity.
`indices` | (integer) vector of monotonically increasing integers.
`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".

### Value

(dataframe) has two columns:

`time` | (numeric)
`intensity` | (numeric)

### 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, imputeChromatogram`

### 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"]]
    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(alignedXIC(XICs.ref[[1]], alignedIndices[,"indexAligned.ref"]), type = "l")

    ## End(Not run)

[Package DIAlignR version 2.2.0 Index]