progTree1: Step 1 for progressive alignment

In shubham1637/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Step 1 for progressive alignment

Description

Step 1 for progressive alignment

Usage

progTree1(
  dataPath,
  outFile = "DIAlignR",
  params = paramsDIAlignR(),
  groups = NULL,
  oswMerged = TRUE,
  scoreFile = NULL,
  peps = NULL,
  runs = NULL,
  newickTree = 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.
groups	(data-frame) contains the run names and their categories/batch id to keep them on the same branch of the tree.
oswMerged	(logical) TRUE if merged file from pyprophet is used.
scoreFile	(string) path to the peptide score file, needed when oswMerged is FALSE.
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, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2021) + GPL-3 Date: 2021-03-03

See Also

progAlignRuns

shubham1637/DIAlignR documentation built on March 29, 2023, 8:45 p.m.