calculateIntensity: Calculates area of a peak in XIC group

Description Usage Arguments Value Author(s) See Also Examples

View source: R/peak_area.R

Description

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

Usage

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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, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

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

See Also

getMultipeptide, setAlignmentRank

Examples

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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.