getGlobalFits {DIAlignR} | R Documentation

## Calculates all global alignment needed in refRun

### Description

Calculates all global alignment needed in refRun

### Usage

    getGlobalFits(
      refRun,
      features,
      fileInfo,
      globalAlignment,
      globalAlignmentFdr,
      globalAlignmentSpan,
      applyFun = lapply
    )

### Arguments

`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.

### Value

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

### Author(s)

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

ORCID: 0000-0003-3500-8152

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

### See Also

`getRefRun, getFeatures, getGlobalAlignment`

### Examples

    dataPath <- system.file("extdata", package = "DIAlignR")
    fileInfo <- getRunNames(dataPath, oswMerged = TRUE)
    features <- getFeatures(fileInfo, maxFdrQuery = 0.05)
    precursors <- getPrecursors(fileInfo, TRUE, "DIA_Proteomics", "experiment-wide", 0.01)
    precursors <- dplyr::arrange(precursors, .data$peptide_id, .data$transition_group_id)
    peptideIDs <- unique(precursors$peptide_id)
    peptideScores <- getPeptideScores(fileInfo, peptideIDs, TRUE, "DIA_Proteomics", "experiment-wide")
    peptideScores <- lapply(peptideIDs, function(pep) dplyr::filter(peptideScores, .data$peptide_id == pep))
    names(peptideScores) <- as.character(peptideIDs)
    ## Not run:
    refRun <- getRefRun(peptideScores)
    fits <- getGlobalFits(refRun, features, fileInfo, "linear", 0.05, 0.1)

    ## End(Not run)

[Package DIAlignR version 2.2.0 Index]