getGlobalFits: Calculates all global alignment needed in refRun
In DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description Usage Arguments Value Author(s) See Also Examples

Calculates all global alignment needed in refRun

getGlobalFits(
  refRun,
  features,
  fileInfo,
  globalAlignment,
  globalAlignmentFdr,
  globalAlignmentSpan
)

`refRun`	(data-frame) Output of getRefRun function. Must have two columsn : transition_group_id and run.
`features`	(list of data-frames) it is output from getFeatures function.
`fileInfo`	(data-frame) Output of getRunNames function.
`globalAlignment`	(string) Must be from "loess" or "linear".
`globalAlignmentFdr`	(numeric) A numeric value between 0 and 1. Features should have m-score lower than this value for participation in global fit.
`globalAlignmentSpan`	(numeric) Spanvalue for LOESS fit. For targeted proteomics 0.1 could be used.

(list) Each element is either of class lm or loess.

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

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-04-19

getRefRun, getFeatures, getGlobalAlignment

dataPath <- system.file("extdata", package = "DIAlignR")
fileInfo <- getRunNames(dataPath, oswMerged = TRUE)
features <- getFeatures(fileInfo, maxFdrQuery = 0.05)
data("multipeptide_DIAlignR", package = "DIAlignR")
## Not run: 
refRun <- getRefRun(multipeptide_DIAlignR)
fits <- getGlobalFits(refRun, features, fileInfo, "linear", 0.05, 0.1)

## End(Not run)