getGlobalAlignment: Calculates global alignment between RT of two runs

In Roestlab/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

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, [e-mail]

ORCID: 0000-0003-3500-8152

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

See Also

getFeatures

Examples

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

Roestlab/DIAlignR documentation built on March 3, 2021, 9:09 a.m.