getGlobalAlignment {DIAlignR} | R Documentation

## Calculates global alignment between RT of two runs

### Description

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

### Usage

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

### Arguments

`oswFiles` | (list of data-frames) it is output from getOswFiles 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".
`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.
`fitType` | (char) Must be from "loess" or "linear".

### Value

An object of class "loess".

### Author(s)

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

ORCID: 0000-0003-3500-8152

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

### See Also

`getOswFiles`

### Examples

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

[Package DIAlignR version 0.99.12 Index]