setAlignmentRank: Set Alignment rank to the aligned feature
In DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description Usage Arguments Value Author(s) See Also Examples

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)