setAlignmentRank {DIAlignR} | R Documentation |
Picks the top feature in run by comparing m-score to unaligned FDR and aligned FDR. If no satisfactory feature is found, peak-integration is carried out by mapping left and right peak boundaries from the reference feature and integrating area under the curve.
setAlignmentRank( multipeptide, ref, eXp, analyte_chr, unalignedFDR, alignedFDR, adaptiveRT, tAligned, XICs.ref, XICs.eXp, integrationType, baselineType, fitEMG, recalIntensity, fillMissing = TRUE )
multipeptide |
(list of data-frames) each element of the list is collection of features associated with a precursor. |
ref |
(numeric) name of the refernce run. |
eXp |
(numeric) name of the experiment run. |
analyte_chr |
(string) coerced transition_group_id. |
unalignedFDR |
(numeric) must be between 0 and maxFdrQuery. Features below unalignedFDR are considered for quantification even without the RT alignment. |
alignedFDR |
(numeric) must be between unalignedFDR and 1. Features below alignedFDR are considered for quantification after the alignment. |
adaptiveRT |
(numeric) defines the window around the aligned retention time, within which features with m-score below aligned FDR are considered for quantification. |
tAligned |
(list) the first element corresponds to the aligned reference time, the second element is the aligned experiment time. |
XICs.ref |
(list) list of extracted ion chromatograms from reference run. |
XICs.eXp |
(list) list of extracted ion chromatograms from experiment run. |
integrationType |
(string) method to ompute the area of a peak contained in XICs. Must be from "intensity_sum", "trapezoid", "simpson". |
baselineType |
(string) method to estimate the background of a peak contained in XICs. Must be from "base_to_base", "vertical_division_min", "vertical_division_max". |
fitEMG |
(logical) enable/disable exponentially modified gaussian peak model fitting. |
recalIntensity |
(logical) recalculate intensity for all analytes. |
fillMissing |
(logical) calculate intensity for ananlytes for which features are not found. |
(NULL)
Shubham Gupta, shubh.gupta@mail.utoronto.ca
ORCID: 0000-0003-3500-8152
License: (c) Author (2020) + GPL-3 Date: 2020-04-13
getMultipeptide, calculateIntensity
data(multipeptide_DIAlignR, package="DIAlignR") data(XIC_QFNNTDIVLLEDFQK_3_DIAlignR, package="DIAlignR") XICs.ref <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["run1"]][["14299_QFNNTDIVLLEDFQK/3"]] XICs.eXp <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["run2"]][["14299_QFNNTDIVLLEDFQK/3"]] ## Not run: # Use getAlignedIndices() to get tAligned. setAlignmentRank(multipeptide_DIAlignR, ref = "run1", eXp = "run2", analyte_chr = "4618", unalignedFDR = 0.01, alignedFDR = 0.05, adaptiveRT = 30, tAligned, XICs.ref, XICs.eXp, integrationType = "intensity_sum", baselineType = "base_to_base", fitEMG = FALSE, recalIntensity = FALSE, fillMissing = TRUE) multipeptide[["4618"]] ## End(Not run)