getGlobalAlignment: Calculates global alignment between RT of two runs
In Roestlab/DIAlign: Dynamic Programming Based Alignment of MS2 Chromatograms

Description Usage Arguments Value Author(s) See Also Examples

This function selects features from oswFiles which has m-score < maxFdrLoess. It fits linear/loess regression on these feature. Retention-time mapping is established from reference to experiment run.

getGlobalAlignment(
  oswFiles,
  ref,
  eXp,
  fitType = "linear",
  maxFdrGlobal = 0.01,
  spanvalue = 0.1
)

`oswFiles`	(list of data-frames) it is output from getFeatures function.
`ref`	(string) Must be a combination of "run" and an iteger e.g. "run2".
`eXp`	(string) Must be a combination of "run" and an iteger e.g. "run2".
`fitType`	(string) Must be from "loess" or "linear".
`maxFdrGlobal`	(numeric) A numeric value between 0 and 1. Features should have m-score lower than this value for participation in global fit.
`spanvalue`	(numeric) Spanvalue for LOESS fit. For targeted proteomics 0.1 could be used.

An object of class "loess".

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

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-12-14

getFeatures

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data(oswFiles_DIAlignR, package="DIAlignR")
fit <- getGlobalAlignment(oswFiles = oswFiles_DIAlignR, ref = "run1", eXp = "run2",
 fitType = "linear", maxFdrGlobal = 0.05, spanvalue = 0.1)