areaIntegrator {DIAlignR} | R Documentation

## 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, shubh.gupta@mail.utoronto.ca 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

[Package DIAlignR version 2.2.0 Index]