progAlignRuns {DIAlignR} | R Documentation

## Peptide quantification through progressive alignment

### Description

This function expects osw and xics directories at dataPath. It first reads osw files and fetches chromatogram indices for each analyte. To perform alignment, first a crude guide-tree is built which can also be provided with newickTree parameter. As we traverse from the leaf-nodes to the root node, runs are aligned pairwise. The root node is named master1 that has average of all fragment ion chromatograms and identified peak-groups. These features are propagated back to leaf nodes and finally aligned features are written in the output file.

### Usage

    progAlignRuns(
      dataPath,
      params,
      outFile = "DIAlignR",
      ropenms = NULL,
      oswMerged = TRUE,
      runs = NULL,
      peps = NULL,
      newickTree = NULL,
      applyFun = lapply
    )

### Arguments

`dataPath` | (string) path to xics and osw directory.
`params` | (list) parameters are entered as list. Output of the `paramsDIAlignR` function.
`outFile` | (string) name of the output file.
`ropenms` | (pyopenms module) get this python module through `get_ropenms`. Required only for chrom.mzML files.
`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.
`newickTree` | (string) guidance tree in newick format. Look up `getTree`.
`applyFun` | (function) value must be either lapply or BiocParallel::bplapply.

### Value

(None)

### Author(s)

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

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-07-10

### See Also

`alignTargetedRuns`

### Examples

    dataPath <- system.file("extdata", package = "DIAlignR")
    params <- paramsDIAlignR()
    params[["context"]] <- "experiment-wide"
    ## Not run:
    ropenms <- get_ropenms(condaEnv = "envName")
    progAlignRuns(dataPath, params = params, outFile = "test3", ropenms = ropenms)
    # Removing aligned vectors
    file.remove(list.files(dataPath, pattern = "*_av.rds", full.names = TRUE))
    # Removing temporarily created master chromatograms
    file.remove(list.files(file.path(dataPath, "xics"), pattern = "^master[A-Za-z0-9]+\\.chrom\\.sqMass$", full.names = TRUE))
    file.remove(file.path(dataPath, "test3.temp.RData"))
    file.remove(file.path(dataPath, "master.merged.osw"))

    ## End(Not run)

[Package DIAlignR version 2.2.0 Index]