setAlignmentRank {DIAlignR} | R Documentation

## Set Alignment rank to the aligned feature

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

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)

[Package DIAlignR version 1.2.0 Index]