setAlignmentRank: Set Alignment rank to the aligned feature

In DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description

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.

Usage

setAlignmentRank(
  multipeptide,
  ref,
  eXp,
  analyte_chr,
  unalignedFDR,
  alignedFDR,
  adaptiveRT,
  tAligned,
  XICs.ref,
  XICs.eXp,
  integrationType,
  baselineType,
  fitEMG,
  recalIntensity,
  fillMissing = TRUE
)

Arguments

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.

Value

(NULL)

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-04-13

See Also

getMultipeptide, calculateIntensity

Examples

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)

DIAlignR documentation built on Nov. 8, 2020, 8:22 p.m.