View source: R/pairwise_pep_peak_corp.R

getAlignedIndices | R Documentation |

This function aligns XICs of reference and experiment runs. It produces aligned indices between refernce run and experiment run.

```
getAlignedIndices(
XICs.ref,
XICs.eXp,
globalFit,
alignType,
adaptiveRT,
normalization,
simMeasure,
goFactor,
geFactor,
cosAngleThresh,
OverlapAlignment,
dotProdThresh,
gapQuantile,
kerLen,
hardConstrain,
samples4gradient,
objType = "light"
)
```

`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". |

`simMeasure` |
(string) Must be selected from dotProduct, cosineAngle, crossCorrelation, 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. |

`kerLen` |
(integer) In simType = crossCorrelation, length of the kernel used to sum similarity score. Must be an odd number. |

`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. |

(data-frame) Aligned indices of reference and experiment runs. Gaps are introduced as NA.

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

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-06-07

`alignChromatogramsCpp, getAlignObj`

```
data(XIC_QFNNTDIVLLEDFQK_3_DIAlignR, package="DIAlignR")
data(oswFiles_DIAlignR, package="DIAlignR")
run1 <- "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
run2 <- "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"
XICs.ref <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[[run1]][["4618"]]
XICs.eXp <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[[run2]][["4618"]]
globalFit <- getGlobalAlignment(oswFiles_DIAlignR, ref = "run1", eXp = "run2",
fitType = "loess", maxFdrGlobal = 0.05, spanvalue = 0.1)
adaptiveRT <- 77.82315 #3.5*globalFit$s
## Not run:
getAlignedIndices(XICs.ref, XICs.eXp, globalFit, alignType = "hybrid",
adaptiveRT = adaptiveRT, normalization = "mean",
simMeasure = "dotProductMasked", goFactor = 0.125, geFactor = 40, cosAngleThresh = 0.3,
OverlapAlignment = TRUE, dotProdThresh = 0.96, gapQuantile = 0.5, kerLen = 9L, hardConstrain = FALSE,
samples4gradient = 100)
## End(Not run)
```

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