areaIntegrator: Calculates area between signal-boundaries.

In shubham1637/DIAlign: Dynamic Programming Based Alignment of MS2 Chromatograms

Calculates area between signal-boundaries.

Description

This function sums all the intensities between left-index and right-index.

Usage

areaIntegrator(
  l1,
  l2,
  left,
  right,
  integrationType,
  baselineType,
  fitEMG,
  baseSubtraction,
  kernelLen = 0L,
  polyOrd = 3L
)

Arguments

l1	(list) A list of time vectors.
l2	(list) A list of intensity vectors.
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.
kernelLen	(integer) length of filter. Must be an odd number.
polyOrd	(integer) TRUE: remove background from peak signal using estimated noise levels.

Value

area (numeric).

Author(s)

Shubham Gupta, [e-mail] ORCID: 0000-0003-3500-8152 License: (c) Author (2019) + MIT Date: 2019-03-08

Examples

data("XIC_QFNNTDIVLLEDFQK_3_DIAlignR", package = "DIAlignR")
XICs <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]]
l1 <- lapply(XICs, `[[`, 1) # time
l2 <- lapply(XICs, `[[`, 2) # intensity
areaIntegrator(l1, l2, left = 5203.7, right = 5268.5, "intensity_sum", "base_to_base", FALSE, TRUE)
# 66.10481 69.39996 46.53095 16.34266 13.13564 13.42331
areaIntegrator(l1, l2, left = 5203.7, right = 5268.5, kernelLen = 9L, "intensity_sum", "base_to_base", FALSE, TRUE)
# 65.01449 71.74432 52.73518 23.84420 17.61869 16.48190

shubham1637/DIAlign documentation built on March 27, 2023, 7:12 a.m.