getGlobalAlignment: Calculates global alignment between RT of two runs

Description Usage Arguments Value Author(s) See Also Examples

View source: R/get_global_fit.R

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

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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

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

DIAlignR documentation built on Nov. 8, 2020, 8:22 p.m.