childXICs: Get child chromatograms from parents

In Roestlab/DIAlign: Dynamic Programming Based Alignment of MS2 Chromatograms

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, [e-mail]

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)

Roestlab/DIAlign documentation built on Feb. 25, 2021, 5:18 p.m.