getAlignObj {DIAlignR} | R Documentation

## Outputs AlignObj from an alignment of two XIC-groups

### Description

Outputs AlignObj from an alignment of two XIC-groups

### Usage

    getAlignObj(
      XICs.ref,
      XICs.eXp,
      globalFit,
      alignType,
      adaptiveRT,
      normalization,
      simType,
      goFactor,
      geFactor,
      cosAngleThresh,
      OverlapAlignment,
      dotProdThresh,
      gapQuantile,
      hardConstrain,
      samples4gradient,
      objType = "light"
    )

### Arguments

`XICs.ref` | List of extracted ion chromatograms from reference run.
`XICs.eXp` | List of extracted ion chromatograms from experiment run.
`globalFit` | Linear or loess fit object between reference and experiment run.
`alignType` | Available alignment methods are "global", "local" and "hybrid".
`adaptiveRT` | (numeric) Similarity matrix is not penalized within adaptive RT.
`normalization` | (character) Must be selected from "mean", "l2".
`simType` | (string) Must be selected from dotProduct, cosineAngle, cosine2Angle, dotProductMasked, euclideanDist, covariance and correlation.
`goFactor` | (numeric) Penalty for introducing first gap in alignment. This value is multiplied by base gap-penalty.
`geFactor` | (numeric) Penalty for introducing subsequent gaps in alignment. This value is multiplied by base gap-penalty.
`cosAngleThresh` | (numeric) In simType = dotProductMasked mode, angular similarity should be higher than cosAngleThresh otherwise similarity is forced to zero.
`OverlapAlignment` | (logical) An input for alignment with free end-gaps. False: Global alignment, True: overlap alignment.
`dotProdThresh` | (numeric) In simType = dotProductMasked mode, values in similarity matrix higher than dotProdThresh quantile are checked for angular similarity.
`gapQuantile` | (numeric) Must be between 0 and 1. This is used to calculate base gap-penalty from similarity distribution.
`hardConstrain` | (logical) If FALSE; indices farther from noBeef distance are filled with distance from linear fit line.
`samples4gradient` | (numeric) This parameter modulates penalization of masked indices.
`objType` | (char) Must be selected from light, medium and heavy.

### Value

A S4 object. Three most-important slots are:

`indexA_aligned` | (integer) aligned indices of reference run.
`indexB_aligned` | (integer) aligned indices of experiment run.
`score` | (numeric) cumulative score of alignment.

### Author(s)

Shubham Gupta, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-12-13

### See Also

`alignChromatogramsCpp`

### Examples

    data(XIC_QFNNTDIVLLEDFQK_3_DIAlignR, package="DIAlignR")
    data(oswFiles_DIAlignR, package="DIAlignR")
    XICs.ref <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["run1"]][["14299_QFNNTDIVLLEDFQK/3"]]
    XICs.eXp <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["run2"]][["14299_QFNNTDIVLLEDFQK/3"]]
    globalFit <- getGlobalAlignment(oswFiles_DIAlignR, ref = "run1", eXp = "run2",
     maxFdrGlobal = 0.05, spanvalue = 0.1)
    AlignObj <- getAlignObj(XICs.ref, XICs.eXp, globalFit, alignType = "hybrid", adaptiveRT = 77.82315,
     normalization = "mean", simType = "dotProductMasked", goFactor = 0.125,
      geFactor = 40, cosAngleThresh = 0.3, OverlapAlignment = TRUE, dotProdThresh = 0.96,
      gapQuantile = 0.5, hardConstrain = FALSE, samples4gradient = 100, objType = "light")

[Package DIAlignR version 1.2.0 Index]