calculateIntensity: Calculates area of a peak in XIC group

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

Description

Retention time from reference run is mapped to experiment run using AlignObj.

Usage

calculateIntensity(
  XICs,
  left,
  right,
  integrationType,
  baselineType,
  fitEMG = FALSE,
  baseSubtraction = TRUE,
  transitionIntensity = FALSE
)

Arguments

XICs	(list) list of extracted ion chromatograms of a precursor.
left	(numeric) left boundary of the peak.
right	(numeric) right boundary of the peak.
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.
baseSubtraction	(logical) TRUE: remove background from peak signal using estimated noise levels.
transitionIntensity	(logical) TRUE: return intensity of each transition, FALSE: return sum of all transitions.

Value

(numeric)

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

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

See Also

getMultipeptide, setAlignmentRank

Examples

data(XIC_QFNNTDIVLLEDFQK_3_DIAlignR, package="DIAlignR")
XICs <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]]
## Not run: 
calculateIntensity(XICs, 5220, 5261, integrationType = "intensity_sum",
 baselineType = "base_to_base", fitEMG = FALSE)

## End(Not run)

Roestlab/DIAlignR documentation built on March 3, 2021, 9:09 a.m.