script2 {DIAlignR} | R Documentation

## Performs alignment using script1 output

### Description

Performs alignment using script1 output

### Usage

    script2(
      dataPath,
      outFile = "DIAlignR",
      params = paramsDIAlignR(),
      oswMerged = TRUE,
      runs = NULL,
      peps = NULL,
      refRun = NULL,
      applyFun = lapply
    )

### Arguments

`dataPath` | (string) path to xics and osw directory.
`outFile` | (string) name of the output file.
`params` | (list) parameters are entered as list. Output of the `paramsDIAlignR` function.
`oswMerged` | (logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
`runs` | (string) names of xics file without extension.
`peps` | (integer) ids of peptides to be aligned. If NULL, align all peptides.
`refRun` | (string) reference for alignment. If no run is provided, m-score is used to select reference run.
`applyFun` | (function) value must be either lapply or BiocParallel::bplapply.

### Author(s)

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

ORCID: 0000-0003-3500-8152

License: (c) Author (2021) + GPL-3 Date: 2021-02-20

### See Also

`alignTargetedRuns`

### Examples

    params <- paramsDIAlignR()
    params[["context"]] <- "experiment-wide"
    dataPath <- system.file("extdata", package = "DIAlignR")
    BiocParallel::register(BiocParallel::MulticoreParam(workers = 4, progressbar = TRUE))
    script1(dataPath, outFile = "testDIAlignR", params = params, applyFun = BiocParallel::bplapply)
    script2(dataPath, outFile = "testDIAlignR", params = params, applyFun = lapply)
    file.remove(file.path(dataPath, "testDIAlignR_script1.RData"))

[Package DIAlignR version 2.2.0 Index]