mstAlignRuns {DIAlignR} | R Documentation

## Peptide quantification through MST 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 guide-tree is built using `mst` which can also be provided with mstNet parameter. As we traverse from the start node to the other nodes, runs are aligned pairwise.

### Usage

    mstAlignRuns(
      dataPath,
      params,
      outFile = "DIAlignR",
      oswMerged = TRUE,
      runs = NULL,
      peps = NULL,
      mstNet = 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.
`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.
`mstNet` | (matrix) array of tree-edges. Look up `getMST`.
`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 (2021) + GPL-3 Date: 2021-05-15

### See Also

`alignTargetedRuns, progAlignRuns, getMST`

### Examples

    dataPath <- system.file("extdata", package = "DIAlignR")
    params <- paramsDIAlignR()
    params[["context"]] <- "experiment-wide"
    mstAlignRuns(dataPath, params = params, outFile = "DIAlignR")
    ## Not run:
    y <- strsplit("run0 run1\nrun2 run2", split = '\n')[[1]]
    y <- cbind(A = strsplit(y[1], " ")[[1]], B = strsplit(y[2], " ")[[1]])
    plot(igraph::graph_from_edgelist(y, directed = FALSE))

    ## End(Not run)

[Package DIAlignR version 2.2.0 Index]