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 2.1.4 Index]