progTree1 {DIAlignR} | R Documentation

## Step 1 for progressive alignment

### Description

Step 1 for progressive alignment

### Usage

    progTree1(
      dataPath,
      params,
      categ = NULL,
      outFile = "DIAlignR",
      oswMerged = TRUE,
      peps = NULL,
      runs = 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.
`categ` | (data-frame) contains the run names and their categories/batch id to keep them on the same branch of the tree.
`outFile` | (string) name of the output file.
`oswMerged` | (logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
`peps` | (integer) ids of peptides to be aligned. If NULL, align all peptides.
`runs` | (string) names of xics file without extension.
`newickTree` | (string) guidance tree in newick format. Look up `getTree`.
`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: 2021-03-03

### See Also

`progAlignRuns`

[Package DIAlignR version 2.2.0 Index]