childXIC {DIAlignR} | R Documentation |
Internal gaps in reference chromatogram and corresponding indices in experiment chromatogram are discarded while merging both chromatogram to obtain a child chromatogram.
childXIC( XIC.ref, XIC.eXp, alignedIndices, method = "spline", polyOrd = 4, kernelLen = 9, splineMethod = "fmm", wRef = 0.5, mergeStrategy = "avg", keepFlanks = TRUE )
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. |
(list) the first element is chromatogram. The second element is aligned parent time-vectors.
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.
Shubham Gupta, shubh.gupta@mail.utoronto.ca
ORCID: 0000-0003-3500-8152
License: (c) Author (2020) + GPL-3 Date: 2020-05-23
mergeXIC, alignedXIC, childXICs
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)