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 fits linear/loess regression on these feature. Retention-time mapping is established from reference to experiment run.

### Usage

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

### Arguments

`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.

### 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

`getFeatures`

### Examples

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

[Package DIAlignR version 1.2.0 Index]