MSTperBatch: Aligns an analyte for a batch of peptides

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

Aligns an analyte for a batch of peptides

Description

For the ith analyte in the batch, this function traverse the MST from start node and align runs pairwise. In the process it updates multipeptide with aligned features.

Usage

MSTperBatch(
  iBatch,
  nets,
  peptides,
  multipeptide,
  refRuns,
  precursors,
  prec2chromIndex,
  fileInfo,
  mzPntrs,
  params,
  globalFits,
  RSE,
  applyFun = lapply
)

Arguments

nets	(list) set of trees ordered for traversal obained from traverseMST.
peptides	(integer) vector of peptide IDs.
multipeptide	(list) contains multiple data-frames that are collection of features associated with analytes. This is an output of getMultipeptide.
refRuns	(data-frame) output of getRefRun. Must have two columsn : transition_group_id and run.
precursors	(data-frame) atleast two columns transition_group_id and transition_ids are required.
prec2chromIndex	(list) a list of dataframes having following columns: transition_group_id: it is PRECURSOR.ID from osw file. chromatogramIndex: index of chromatogram in mzML file.
fileInfo	(data-frame) output of getRunNames.
mzPntrs	(list) a list of mzRpwiz.
params	(list) parameters are entered as list. Output of the paramsDIAlignR function.
globalFits	(list) each element is either of class lm or loess. This is an output of getGlobalFits.
RSE	(list) Each element represents Residual Standard Error of corresponding fit in globalFits.

Value

invisible NULL

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2021) + GPL-3 Date: 2021-05-15

See Also

mstAlignRuns, alignToRefMST, getAlignedTimesFast, getMultipeptide

Examples

dataPath <- system.file("extdata", package = "DIAlignR")

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